Protein Structure Prediction Center
Message Board
Deadline to register for CASP11 is approaching!(2014-10-24)
Dear CASP Participants and Enthusiasts:

The final deadline to register for CASP11 is fast approaching! Rates are guaranteed only until November 1. After that they may increase to accommodate standard hotel prices, which are considerably higher. So if you have not already signed on, now is the time!

It promises to be an interesting meeting. In addition to all the usual fun of the fair, there will be sessions covering the new features of this CASP experiment, including modeling aided by experimental sparse data (X-linking and simulated NMR) and the CASP-CAPRI joint experiment on prediction of protein complexes. And early assessment results suggest exceptional results.

We are also delighted to announce that we have been able to upgrade the accommodation for the meeting without increasing the cost for you. We are moving to Iberostar Maya, a hotel that is part of the same Iberostar Paraiso all inclusive complex (located on the Riviera Maya, 25 min from Cancun airport).

We look forward to seeing you in this exciting new CASP location in December.

CASP organizers
Voting for the Methods Talks(2014-10-23)
Dear CASPers,

This message announces start of the voting on the Methods Talks. Please cast your votes for the methods you consider worth presenting at the meeting at http://predictioncenter.org/casp11/voting.cgi. For your convenience, we compiled a book of selected abstracts that contains communications just from the nominated groups (http://predictioncenter.org/casp11/doc/CASP11_Abstracts_nominated.pdf).

The voting facility will be open until Monday, Nov. 10. You should be able to track the voting summary after you cast your vote(s). Please refrain from voting for your own method or that of your close collaborators.

Authors of the methods that fared the most interesting for the community will be invited to talk at the CASP11 meeting.

CASP Organizers
Candidates for methods talks(2014-10-13)
Dear members of the CASP community,

As in previous two CASPs, in CASP11 we plan to have "methods talks" that would not be based entirely on group performance, but rather present new interesting ideas in the field.

Now, when the CASP11 Abstract book is available online (predictioncenter.org/casp11/doc/CASP11_Abstracts.pdf), we ask you to familiarize yourself with the descriptions of CASP11 methods, and nominate those of them that you consider innovative, having potential to improve the field, or otherwise interesting. Please send us an email with your nominee(s) by the next Monday, October 20. We will summarize your suggestions and provide you a list of the most interesting methods for voting.

CASP Organizers
Final week of submitting abstracts(2014-9-12)
Dear CASP predictors,

For inclusion your contribution in the CASP11 Abstract Book, please make sure your abstract(s) reach us not later than the next Friday, September 19.

CASP organizers
Early bird registration deadline extended for one more day(2014-9-4)
Due to organizational reasons, we are moving the early bird registration deadline forward by 24 hours. You have time by the end of Friday, September 5, to register for CASP11 meeting at the discounted rate.

CASP organizers
Reminder - only three days left to save on CASP11 registration(2014-9-2)
Dear CASP participants,

This is a friendly reminder that the Early Bird registration for the December in Mexico meeting ends in three days. If you want to take advantage of the discounted registration rates - please act quickly - the rates will go up $250 per person starting September 5.

CASP organizers
You can send us your methods abstracts now(2014-8-20)
Dear predictors,

Yesterday three events were marked on the CASP11 calendar.

1. We received the last CASP11 prediction. Thanks for all your hard work over the period of three and a half months! Now you can take a well deserved rest and we (organizers and assessors) will concentrate on assessing your almost 60000 predictions.

2. We opened the webpage for collecting methods abstracts. Please read the instructions carefully and address all the questions specified in the Abstract submission form (http://predictioncenter.org/casp11/abstracts.cgi). You have one month to compose and send us your abstracts. Please remember that, as usually, your contributions will be taken into account in choosing presentations for the meeting.

3. We stopped accepting applications from students /minorities for financial support to attend the CASP11 meeting. The organizing committee will consider your applications and notify fellowship recipients shortly after the closing of the "early bird" registration window - tentatively in the second decade of September.

Please be reminded that you have only two more weeks to take advantage of the discounted registration rates for the meeting. The rates will go up on September 5th.

CASP organizers
Last targets in contact-assisted category(2014-8-11)
Dear CASPers,

1. This week we are releasing the last 6 targets in contact-assisted categories Ts and Tc. Three of these targets (Tc826, Tc827 and Ts812) will be released today after closing the corresponding contact-assisted targets from the previous round, two more targets (Tc806 and Tc835) will be released tomorrow, and the last one - Tc832 - on Wednesday. Deadline for today's targets will be next Monday, August 18, and for the remaining three - August 19.

2. On the same day (August 19) we will stop accepting applications from students /minorities for financial support to attend the CASP meeting. Requirements for submitting the applications are available at the meeting registration page.

3. Shortly after receiving the last prediction (next week) we plan to start collecting methods abstracts. The Abstract Submission web page will be available through a link from the CASP11 main page.

CASP organizers
End of CASP11 regular prediction season(2014-8-1)
Dear CASP predictors,

Yesterday we closed the last three regular CASP11 targets. All in all, we released 100 targets including 55 all-group targets, and collected over 55,000 predictions. Thanks a lot to all of you, whose hard work and dedication made CASP11 yet another successful protein structure prediction experiment. The Prediction Center and the assessors already got access to many of the CASP11 structures and are in the process of evaluating the submitted models.

Even though the prediction season is over for the regular targets, the action is still in full swing for the special experiment targets. Today we have released the last targets in refinement (TR) and contact-assisted (Tp) categories. Also, no more targets will be released in the cross-linking assisted category (Tx). Summarizing, in CASP11 we have released 37 refinement targets (cf 28 in CASP10), 24 Tp targets (cf 15 in CASP10) and 4 Tx targets (new category).
Through August 11, we will continue posting tasks in Ts and Tc categories for those targets, where Tp and Tx challenges are currently active. The last CASP11 submission deadline in the assisted categories is planned for August 18.

CASP organizers
Updated file for Tx812(2014-7-24)
Dear Tx predictors,

Please update the input file for target Tx812. The originally posted file was fine except it included a few contact pairs to non-existing residues 250-254 (should be 200-204 instead). If server groups want us to send a separate modeling request for this target - please let us know.

Thanks,
CASP organizers
CASP11 meeting registration is now open. (2014-7-24)
We are opening registration for the CASP11 meeting.

The discounted early bird cost is $1100 per person in a separate room and $950 in a shared room (double occupancy), if registration is completed by September 4. This includes registration fee, hotel accommodation and all meals for the time of the Conference. Participation fees will go up after September 4 to $1350 (separate room) and $1200 (shared).

We have negotiated discounted rates for extra nights and accompanying persons. Details are available at the UC Davis Conference Services registration page (link to which is provided at the bottom of the CASP11 meeting registration page - http://predictioncenter.org/casp11/meeting.cgi).

Please follow the registration guidelines closely. We reserve the right to cancel any registration not adhering to the guidelines, even when the system completes the registration and accepts payment.

We expect some funding for financial assistance to students and minorities, as well as to the most successful predictors. Awards will be made in the form of reimbursements for registration and/or accommodation costs starting in mid-September. Only registered participants will be considered for fellowships. To apply for a student/minority fellowship - please send us an email describing your role in developing CASP-participating method(s) and specify what you expect to gain from coming to the CASP meeting (one-two paragraphs). Please attach your short CV and specify the subject of the message as: CASP11 fellowships - yourname, groupname. The applications will be accepted until August 19, 2014.

CASP organizers
T0835, T0837 - reopening for human prediction(2014-7-15)
Targets T0835 and T0837, which were originally released as server-only targets, appeared to be more difficult for prediction than originally estimated and we are reopening them for human prediction and giving expert groups 10 more days for the modeling.

CASP organizers
CASP11 - week 12 update(2014-7-11)
=== Week 11 summary
We have finished the last full week of CASP11 target release with 95 targets and over 45,000 predictions.

=== Next week plans
We plan to release last five regular CASP11 targets next week Monday through Wednesday. One of these targets will be an all-group target, the rest - server only. After July 16 we will be releasing only refinement and contact-assisted targets.

=== Thank you to protein structure determination community
With the last targets already set for release, we are on our way to finish CASP11 season with 100 targets sharp! It was not an easy task for organizers to get such a rich testing set for you under the conditions of slowing PSI structure determination activity. Here we would like to take an opportunity and thank every single one crystallographer and NMR spectroscopist who participated and provided targets, be it one or thirty. The big share of targets was again obtained from the Structural Genomics centers, and we want to thank them for their continuous support of CASP. In particular, we want to recognize the JCSG, which provided over 30% of all CASP11 targets (see http://predictioncenter.org/casp11/numbers.cgi). We are also happy to report that 40% of the targets came from the non-SGI research groups, twice as many as in CASP10 and more than 3 times as many as in CASP9.

=== Meeting registration - update
Due to technical problems with the secure meeting registration page, we had to postpone opening of the meeting registration till the next week. A separate announcement will be sent once the meeting registration page becomes available.

CASP organizers
Tx781 - expires tomorrow(2014-7-7)
The first Tx target expires for prediction tomorrow. Below we provide some additional information regarding the cross-linking experiments that have been performed. Hope this information may be useful for predictors.
***
The cross-linker is hetero-bifunctional and reacts on one side with the side chains of K, S, T, Y via the amide and hydroxyl group, respectively. On the other side the cross-linker reacts indiscriminately with any C-H and N-H bond, be it in the side chain or backbone of any amino acid.
CASP11 - week 11 update(2014-7-3)
=== Week 10 summary
No targets will be released tomorrow, and we are finishing tenth CASP11 week with 85 targets and over 39,000 predictions.

=== Next week plans
We are almost done with releasing regular targets in CASP11. Next week will be the last full week of target release. We will suggest you another 10 targets, two per day, Monday through Friday. Four of these targets may be suitable for CAPRI. More targets are expected in the refinement and contact-assisted categories.

=== Meeting registration
We plan to start registration for CASP11 meeting next week. A separate announcement will be sent once the meeting registration page becomes available.

CASP organizers
Tx781 - extended prediction deadline (2014-7-1)
As promised, we are extending prediction window for Tx781 by one more week (until July 8).

CASP organizers
CASP11 - week 10 update(2014-6-27)
=== Week 9 summary
Ninth week concluded with 77 targets released and over 35,000 predictions accepted.

=== Cross-linking assisted targets; Tx781
This week we released the first x-linking-assisted target. Please be advised that the reported distance limit (25 Angstroms for Tx781) is between the CAs of corresponding residues.

Target Tx781 was released yesterday on a short prediction deadline as T0781"s structure was scheduled to appear in the PDB on July 2. Today we got the information that the coordinates will not be released on that date and thus we might be able to offer you one more week for prediction. To play it safe and be insured from any last minute surprises, we want to keep the July 1 deadline for now and encourage you to submit your predictions by that date, keeping in mind that most likely the deadline will be extended on July 2.

=== Next week plans
Eight regular targets will be released next week: two targets per day Monday through Thursday and no targets on Friday. Three of the next week targets may be suitable for CAPRI. Please pay attention to the posted information on the Wednesday targets T0840 and T0841 as they constitute a single heterodimer modeling entity. More targets are also expected to be released in the refinement and contact-assisted categories.

CASP organizers
T0796 re-release - STOPPED(2014-6-27)
Dear predictors,

Please disregard our earlier message on re-release of T0796 for human prediction. It will stay a server-only target and no additional experiments (refinement or contact-assisted) are planned for it.

CASP organizers
First Tx target - Tx781 has been released with only 5 days for prediction(2014-6-26)
Dear Predictors,

We are beginning a special experiment in contact assisted prediction to allow using actual experimental data (distance constraints from cross-linking experiments) to facilitate obtaining correct models (Tx targets). Considerable effort was put into making these tests possible (thanks to Juri Rappsilber"s experiments and cooperation from crystallographers providing protein samples). Normally, we will be giving you at least a full week for prediction of Tx targets. With this target, though, comes a shorter deadline as the structure will most likely be released by the PDB on July 2. We will inform the assessors about the shorter deadline for Tx781 and this may be taken into consideration in the assessment. Nevertheless, since we expect at most a few targets in this category, all the results will make part of CASP11 and be discussed at the meeting.

The released file is in the usual CASP contact data format. Due to the length of the linker, the limits are of up to 25 rather than the usual 8 Angstroms. The last column provides an estimated confidence level for the contact to be correct.

CASP organizers
CASP11 - week 9 update(2014-6-20)
=== Week 8 summary
Eighth week concluded with 69 targets, over 30,000 predictions and over 200 groups participating. Last Wednesday PDB has released a big batch of CASP targets. All these targets are marked with PDB codes in the Description column of our Target List. Those anxious to see how accurately they predicted these targets can compare now their models with the experimental structures.

=== Next week plans
Eight regular targets will be released next week. We will have two targets on Monday, Thursday and Friday and only one long and difficult target on Tuesday and Wednesday. No CAPRI targets planned for this week. More targets are expected to be released in the refinement and contact-assisted categories. We also hope to get data for the first target in Tx category (cross-linking assisted prediction).

CASP organizers
CASP11 - week 8 update(2014-6-13)
=== Week 7 summary
The FIFA World Cup has started, but we continue releasing targets :) . Seventh week concluded with 61 targets, over 24,000 predictions and just short of 200 groups participating.

=== T0803 re-release (June 13)
Target T0803 (originally server-only target) has been released for human prediction today with the June 24 deadline.

=== CASP11 disorder prediction termination
At the CASP10 predictors' meeting in Gaeta the community decided that we should proceed with the disorder prediction in CASP11 only if suitable targets will be available. The organizers tried hard to get the proper targets for disorder prediction, but all our efforts were unsuccessful. Under such circumstances we announce that we are terminating CASP11 prediction of disorder regions and apologize to the predictors, who invested their time in this category of prediction.

=== Next week plans
Eight regular targets will be released next week. We will have two targets Monday through Wednesday and only one target (but long and difficult) on Thursday and Friday. Please pay attention to the provided additional info, especially for the Wednesday target, T0825. The interest in modeling of this target will lie completely in predicting the dimer.

More targets are expected to be released in the refinement and contact-assisted categories.
CASP11 - week 7 update(2014-6-6)
=== Week 6 summary
We have finished sixth week with 51 targets released, 194 groups contributing, and over 19,000 predictions submitted.

=== Contact assisted prediction
The first two Ts targets (Ts761 and Ts763) are to expire on June 11, and we will release Tc challenges for the corresponding targets immediately afterwards. (reminding that Tc-type targets are those, where we will be providing information on the correctly predicted contacts in RR category). We want to warn you that we will have only 6 days for prediction of these two specific targets, as both of them will be released by the PDB on June 18.

=== Refinement targets
With two refinement targets released today, we are already at the mark of 11 TR targets. Note that today's targets, TR780 and TR280, come from two different domains of the same regular target, T0780. The two domains have a similar fold, but models for them have problems in different regions, and therefore we decided to release both as TR targets.

=== Next week plans
Next week we will release ten more regular targets, one harder and one easier per day. Four targets will be designated as CAPRI targets. We also expect more targets to be released in the refinement and contact-assisted categories.

CASP organizers
CASP11 meeting location (2014-6-5)
Dear CASP Participants,

We are happy to announce a new site for the CASP 11 meeting scheduled for December 7-10, 2014. The conference will be held at Paraiso Lindo hotel on the Riviera Maya, Mexico (http://www.iberostar.com/en/hotels/riviera-maya/iberostar-paraiso-lindo).

This may come as a surprise to those who saw our earlier announcement of the conference site in the Dominican Republic. The response from the CASP community was better than expected, and we decided to move the conference to a larger site. Although the resort on the Riviera Maya is normally more expensive, the Iberostar organization agreed to grant us the same favorable conditions that allow keeping the conference registration fees at the original level (for registration and all-inclusive accommodation in a double occupancy room - $950, single - $1100). The resort is conveniently accessed via Cancun International airport.

In compliance with the NIH requirement, the Paraiso Lindo hotel is family friendly. The special conference hotel rates will be available three days before and three days after the meeting. Registration for the conference is expected to open on July 1.

In addition to the climate and the sea, the Yucatan peninsula offers numerous attractions:
http://www.tripadvisor.com/Attractions-g659488-Activities-Riviera_Maya_Yucatan_Peninsula.html
http://www.visitmexico.com/en/mayan-riviera

We hope to see you all at CASP11 at the beautiful Paraiso Lindo.

CASP organizers


T0774 - reopening for human prediction(2014-6-2)
Target T0774, which was originally released as a server-only target, expired for prediction today (June 2). We have carried out preliminary evaluation of this target and it appeared to be more difficult than originally estimated. Therefore we are reopening T0774 for human prediction and giving expert groups 10 more days for modeling.

CASP organizers
First Ts target - Ts761(2014-6-2)
Dear predictors in contact-assisted categories,

With this message we want to bring your attention to the release of the first sparse experimental data assisted target - Ts761.


We expect that the new prediction experiment will show if data available in a typical NMR structure determination process can help improving the quality of structure models. For the Ts type of targets, we will be releasing information on simulated sparse NMR contacts that reflect the data available in the initial stages of the state-of-the-art NMR study of a large protein. The corresponding input files will be posted at predictioncenter.org/download_area/CASP11/extra_experiments/. Please note that some restraints in the released contact lists are ambiguous. For each NOESY peak, one or more distance restraints are provided, of which at least one is correct. Format of the Ts input file is similar to the CASP's RR format - please consult the README_Ts file (uploaded to the same directory as above) for a more detailed description.

CASP organizers
CASP11 - week 6 update(2014-5-30)
=== Week 5 summary
We are finishing fifth week of CASP11 prediction with 40 targets released, 180 groups contributing, and 14,500 predictions submitted.

=== Cancellations
We had to cancel a very interesting target, T0791. It was solved by a competitor group and released with the PDB past Wednesday, May 28. Since the premature PDB release happened after the server deadline, we are canceling this target only for human and QA prediction. All server predictions and all DR predictions will be evaluated as usually.

=== Contact assisted prediction of tertiary structure
This week we released the first four targets (Tp761, 763, 767, 771, "p" stands for predicted) in the contact-assisted category. Next week we plan to release corresponding Ts targets ("s" stands for sparse) for two of those targets (761 and 763), and the following week - corresponding Tc targets ("c" stands for correct). Below we recapitulate the principles of contact-assisted prediction in CASP11.

In the current CASP, the contacts that we are releasing following the primary CASP 3D structure modeling experiment on a given target (i.e. the unassisted prediction) are different than those in CASP10. The general idea is to include more realistic scenarios where restraints are obtained from typically accessible sources (Tp, Ts and Tx below), rather than selected from structure. In addition we will also be providing sets of contacts selected with the knowledge of structure (Tc, below). The contact sets will be released only on targets without a clear homology to available structures, and will include:

Tp: Predicted three dimensional contacts, collected in the Contact Prediction (RR) category - release shortly after finishing the unassisted prediction;
Ts: Sparse NMR contacts (simulated, see below) - release immediately after finishing the Tp prediction (if not selected for Tx);
Tc: Predicted three dimensional contacts as in (A), but selected to include only correct contacts - release immediately after finishing the Ts prediction;
Tx: Contacts obtained from cross-linking mass spectroscopy studies (expected only in a few cases, where it is possible to collect experimental data) - release after the x-linking data is available; targets selected for the Tx dataset will not be used in Ts and Tc sets.

Simulated sparse NMR contacts: Provided contacts will be based on simulations carried out in Gaetano Montelione"s group (CASP10 assessor) and will reflect data available in the initial stage of an NMR study. For fairly large proteins (> 160 AA), typically data are collected on deuterated samples resulting in simplified spectra that are easier to assign. The corresponding constraints are sparse and usually not sufficient to refine the structure using standard NMR packages. The challenge for us is to either solve the structure using more sophisticated modeling techniques or to provide at least partially correct models, facilitating interpreting more complex NMR data sets.

X-linking studies: Contacts from x-linking mass spectrometry will be obtained from studies carried out in Juri Rappsilber"s group (Technical University of Berlin). We are actively pursuing these experimental datasets and currently have several targets lined up. Although we will do our best to obtain these datasets for CASP, we have to caution that at present none have been completed.

=== Refinement targets
Four more targets have been released this week in the refinement category.
Last week we warned you about the short deadline for one of the TR targets, TR759. The NESG Center (target source) and the PDB both agreed to extend the hold for T0759 for two more weeks, and now we can offer refinement groups the full 3 weeks for TR759 modeling (deadline has moved from June 2 to June 12).

=== Complexes
This week we released another hetero-multimer for prediction (T0797/798 tandem). Please check submission instructions in the "Additional information" section for these targets.

=== Next week plans
Next week we open the overall ninth hundred of CASP targets with release of 10 regular targets: T0800-T0809. As usually, we will have one harder and one easier target per day. Three targets will be designated as CAPRI targets. We also expect more targets to be released in the refinement and contact-assisted categories.

CASP organizers
CASP11 - week 5 update(2014-5-23)
=== Week 4 summary
CASP11 is running full sail as we are finishing the forth week of prediction. With 34 targets released and 175 groups contributing, we have crossed the 10,000 prediction mark today.

=== Refinement targets
This week we released one target in the refinement category, TR759. Some of you have noticed that we are on a tight schedule with this target expecting predictions not later that June 2. Unfortunately, that is all we can offer as the structure will be released from the PDB the very next day. Cases like that (shorter deadlines) may happen in the future (so always pay attention to the deadlines!), but one may expect them as exceptions rather than a rule.

=== Multimers
This week we released two hetero-multimers for prediction (T0787/788 tandem and T0791). Hetero-multimers are new for CASP, and we posted detailed instructions on how to submit the predictions in the "Additional information" section for specific targets. Nevertheless, we received two messages asking for further clarifications, and we thought that answers to them may be useful to a wider audience.

*Question 1. Our group is a human group and we predict only all-group targets. T0787 is an all-group target, but T0788 is server-only. What are we supposed to do here?
*Answer 1. If you predict only monomers for all targets, then you do what you usually do - submit your model for T0787 and ignore T0788. If your method is capable of predicting multimers, submit your prediction for both T0787 and T0788 before the "human" expiration deadline.
*Explanation 1. We designate targets as server-only if their monomeric prediction is expected to be easy and not worth spending the time of human groups. Target T0788 is one of such targets. It has a very high sequence identity to available structures (misses just a few residues) and the main interest lies in prediction its multimeric state in the T0787/788 complex. Therefore, human groups will be assessed on this target only in the context of predictability of the whole T0787/788 hexamer (we will ask CAPRI team to do this evaluation job for us). Another example is target T0792. This target seems to be quite easy for monomeric prediction but shows quite unusual dimerization. Therefore it was released as a server-only target, which nevertheless may be a very interesting target for human experts predicting quaternary structures.

In general, we encourage human groups to predict multimeric targets ("Oligo State" column >1 in the Target List) regardless of their status (all-group or server-only). Please refer to the Targets section in the description of CASP11 experiment (predictioncenter.org/casp11/) for details.

*Question 2. The T0787 and T0788 target descriptions say that we should concatenate the two trimers in a single file.
* Answer 2. No, you should submit models for these two targets in separate files as for usual CASP targets. What we meant was that we expect to get a full set of coordinates in the same frame of reference after we concatenate your respective models T0787TSxxx_1 and T0788TSxxx_1.

=== QA
We have canceled server-only target T0778 for QA prediction as its structure was solved by a non-CASP experimental group and released by the PDB this week. Server predictions in other categories are not affected by this premature release and will be assessed as normal.

=== Next week plans
Next week we will release 7 regular targets. On Monday, Tuesday and Friday we will post only one target, each of which will be relatively large (400+ residues) and not that easy for modeling. Wednesday will be as usual (one harder and one easier target) and on Thursday we plan to release another hetero-multimer (T0797/798) - please pay close attention to the additional information posted for these targets.

CASP organizers
CASP11 - week 4 update(2014-5-16)
We have finished three weeks of CASP11 with 24 targets released and over 6,000 predictions collected from 111 groups.

This week we released first two targets in the refinement category, TR760 and TR762. Please note that for the refinement targets we are not sending automatic queries to servers. If you want your server to receive automatic queries for refinement targets - please let us know and we will accommodate your request.

For the next week we have 10 more regular targets for you. Please check additional information that will be provided with the targets, especially for the two planned for the Wednesday release - T0787 and T0788. We also hope to release 1-2 extra experiment targets, most likely in the refinement category. Next week (Tuesday) we also close our first human target - T0759. Please be reminded that assessors may want to know which servers you used as starting points for your expert modeling and what useful things you can say about your specific models (see our previous messages). Ta make additional information in your predictions better searchable, please use

REMARK 1 for identifying starting server models

and

REMARK 2 for listing your model-specific comments.

These comments will be stripped from your predictions for the original evaluation (so that your identities are not revealed in any way to the assessors), and will be shown to the assessors only after they come up with their final conclusions on the results.

CASP organizers
CASP11 - week 3 update(2014-5-9)
We have finished two weeks of CASP11 with 14 targets released and over 2,500 predictions collected from 100 groups (out of almost 200 registered). For the next week we will have 10 more targets for you.

We want to remind you that we are publicly releasing the best 150 server models per target on the 8th day after the target release. The predictions are selected to this "best 150" list based on the results of the Prediction Center's a-priori model quality assessment method. The files with the best 150 models have the "stage2" suffix in their name, e.g. T0759.stage2.3D.srv.tar.gz. The tarballs are posted at http://predictioncenter.org/download_area/CASP11/server_predictions/ around noon PDT. CASP and CAPRI participants are welcome to use these models as starting points for their modeling with a credit to original servers. All server models are posted on the same web page 2 days after the "best 150" posting.

CASP organizers
Assessing biological relevance of models(2014-5-5)
Dear CASPers,

The first two days of CASP11 are behind us and we are starting a new prediction week.

As we informed you earlier, the assessors in CASP11 will try their best to assess the models from the perspective of how well these models address relevant biological questions. The things that assessors might be looking at are:

What a 3D model can tell about biological properties of a protein that a simple sequence alignment does not show?
What super family does this protein belong to?
What does a specific mutation do to structure and function?
Where/how does protein partner X interact?
Which residues should be mutated to disrupt interaction with binding partner X?
What is the binding specificity of this member of the protein family?
What loops might make good epitopes?
Where/how does molecule X bind?
Where are the domain boundaries?
How does alternative splicing affect structure and function?

We realize that these questions cannot be reliably answered without staging additional experiments (which is unlikely) and we do not expect these questions to be applied for all targets. But we do expect that at least for some of them the assessors will be able to provide their educated guesses and expert judgements on the listed subjects. For some targets, we may provide specific information that we have from the target providers (e.g., reason for solving the structure, why it is important, oligomerization state, any ligands bound, etc.) hoping that you might be able to use this additional info in your modeling approaches and, potentially, do something differently knowing these extra bits of information.

We are also encourage you to provide one-two lines of text in the REMARK field (especially for hard, likely New Fold targets) listing useful things that you can say about the specific model. Especially, assessors will be interested to hear what experiments can you suggest from unique properties of YOUR model (that "default" modeling methods don't have) that would possibly interest biologists.

CASP organizers
WeFold announcement(2014-4-29)
The WeFold collaborative effort will run again this year for CASP11 and we would like to invite members of the CASP community to join in. This collaborative experiment lets different groups work on different components of the protein structure prediction pipeline (like contact predictions, sampling, refinement, and scoring) thus making it possible to leverage the diverse expertise of the participating groups. The collaboration is mediated by the science gateway http://wefold.nersc.gov that was developed by the National Energy Research Scientific Computing Center (NERSC) which also provides the computing resources. Thirteen labs participated in CASP10 using up more than 1.6 million computing hours and sharing 8.8 million models. We expect to have even more participants this year. You can see the list of participants so far here: http://wefold.nersc.gov/wordpress/about.

This year, WeFold is reaching out to the broader community of scientists. Besides our machine-learning experts who are also CASP participants, we are engaging members of the broader machine-learning community to help us develop new scoring functions. We plan to have a formidable selection of scoring functions that will be applied to the ranking of the hundreds of thousands of models shared by the WeFold community. To learn more about the project, please visit the WeFold gateway http://wefold.nersc.gov or contact Silvia Crivelli at SNCrivelli@lbl.gov.
May 1 - start of CASP11(2014-4-29)
Dear predictors,

As of today, over 150 groups are ready to start their CASP11 prediction marathon. If you are planning to participate, but have not registered yet - please do this as soon as possible. Tomorrow is also the last chance for server curators to resolve any remaining issues with connectivity of their servers to CASP distribution/ verification servers.

We will start CASP11 slow and release two relatively easy targets on the first day of prediction season, May 1. Two more targets (including a challenging one) will be released the next day, and 10 more - the next week, Monday through Friday. We are planning on keeping this pace of two targets per day for the whole CASP11 prediction season (subject to target availability).

For those of you, who plan to submit multimeric predictions and want to have them evaluated in CAPRI, please be reminded that CAPRI-eligible targets may be selected from both all-group and server-only targets. Therefore, if you registered a regular (non-server) group - please make sure that you submit your predictions on all CAPRI-eligible targets, including CASP11 server-only targets. Note that the human expiration date on server-only targets will be shorter than that on all-group targets and usually set to 10 days after the target release.

Wish you a great prediction season!

CASP organizers
CASP11 dry run for servers(2014-4-15)
Dear CASP participants,

Registration for CASP11 is currently under way and more than 60 research groups have already registered for the experiment. We are starting checking connectivity and correctness of prediction format for the servers in TS, RR and DR prediction categories on Thursday, April 17. Quality assessment (QA) servers will be tested next week. Therefore, if you plan to participate in the server track but have not registered your server(s) yet - we advise you to do so ASAP. We will be sending your servers a request to predict a test target, which, obviously, will not be a part of the CASP11 experiment. Please consult our format page (http://predictioncenter.org/casp11/index.cgi?page=format) for prediction format details.

CASP organizers
CASP11 registration opens March 31(2014-3-30)
Dear CASP Participants,

Exiting news: new CASP experiment is just around the corner! We hope that you are full of enthusiasm and anxiety (as we are) and have your computers greased and warmed up. The registration for CASP11 opens tomorrow, March 31, and the link to the registration pages will be available from the CASP11 main page:
http://predictioncenter.org/casp11.

Based on your feedback and keeping pace with the new developments in the field, we are refocusing the experiment by launching additional prediction challenges and introducing important changes to assessment. Detailed description of the experiment is available at the CASP11 main page; here we list the main changes that will be implemented in CASP11.

1. Assessment.
In refocusing towards greater emphasis on function, submitted models will be assessed on of how well they address relevant biological questions. We will do our best to present these questions to you up front. To this end we will collect the relevant information from target providers and their collaborators (reasons for solving the structure, functionally important regions, oligomerization state, any ligands likely to be bound, etc.). The assessors, especially the assessor in the template-based category, will analyze which models are the most helpful in clarifying these questions. In addition, the standard numerical evaluation of predictions will be carried out at the Prediction Center.

2. Collaboration with CAPRI (Critical Assessment of Protein Interactions).
We want to bring closer the two related communities with the aim of stimulating increased interest in modeling of protein interactions. Members of both the CASP and CAPRI communities will be invited to model the interfaces of protein complexes, homo-multimers and domain interactions in appropriate CASP11 targets (this will not require separate submissions, only the usual CASP predictions in the TS format). The results will be evaluated using the established CAPRI criteria. We plan to discuss the results of both experiments at the CASP11 conference.
The results will be evaluated using the established CAPRI criteria. We plan to discuss the results of both experiments at the CASP11 conference.

3. Details of prediction.
New assessment standards and challenges require additional information to be included in model submissions.
3.1. Specifics of the new function-oriented assessment (described in 1 above) requires inclusion of all ligands /co-factors in the submitted models. These ligands should be listed in the end of the model as HETATM records placed between the last TER and final END (details will be posted at the format page shortly).
3.2. In connection with item 2 (above), we strongly encourage submission of predictions as multimers, when applicable (information about the oligomeric state will be provided when available), so that the accuracy of inter-chain interfaces may be evaluated in CAPRI.
3.3. Following suggestions of CASP10 predictors meeting, we will request sensible prediction of atom errors (the B-factor column) in the TS predictions (predictions with fewer than 2 different B-factors will be rejected). A more judicious prediction of accuracy will help in assessing how useful is the model in answering biological questions.

4. New initiatives.
We will continue probing the extent to which sparse experimental data or contact predictions might improve the accuracy of models. For selected targets we will provide contact data obtained from prediction, experiment, or generated to simulate sparse experimental data. We plan to make available the following tests:
4.1. Modeling based on predicted contacts.
Following the regular target prediction, we will be releasing the top ~L/5 long-range contact predictions from the historically best CASP contact-prediction groups (L- target length). These predictions will be released for some of the more challenging targets and will include both correct and incorrect contacts. The aim of this exercise is to learn if contact predictions from the existing methods can help improve the quality of submitted models.
4.2 Modeling based on simulated sparse experimental data.
Following 4.1, we plan to release a bigger set of contact predictions simulated based on the target structure (provided we can obtain the coordinates in advance and have enough time for re-prediction). As in 4.1, the provided sets will contain both correct and incorrect contacts. The aim of this exercise is to learn if contact information from sparse experimental data can help improve the quality of structure models.
4.3. Structure prediction based on only the correct predicted contacts (filtered 4.1).
Will take place after completing 4.2. We will be releasing top ~L/5 correct long-range contacts from the historically best CASP contact-prediction groups. The aim of this exercise is to learn if contacts that can be identified by the best contact-prediction methods can help improving quality of structure models.
4.4. We are also exploring an option of obtaining real cross-linking data on selected CASP targets (using biological material from structure providers). If we succeed, we will provide these restraints in a separate test.
4.5. Evaluation of models based on a perfect alignment to the template.
For the TBM targets with significant alignment errors seen in the submitted models, we will be releasing the correct alignment to the best structural template found with the LGA program (please comment on what format of the input data would be the easiest to incorporate in your methods - LGA output, AL CASP format, FASTA format alignment). Obviously, this experiment also requires that the target structures are available at the time.

5. The meeting.
At the last two CASPs many of you suggested exploring new sites for the meeting. We listened and are taking the next CASP to a completely new location - the Caribbean. The price of attendance will be lower than that currently offered at Asilomar and the airfare for most participants will be comparable.

If you have questions /comments /reservations about the registration and the suggested changes - please let us know by replying to this message. Especially, we are interested in your relative level of interest in the contact assisted tests as outlined in Section 4 above.

Thanks for your interest - we hope for an exciting new CASP!

CASP organizers
Resuming CASP ROLL(2013-1-22)
Dear CASPers,

Best regards for all of you in the New Year!

Hoping that you had good rest after the CASP10 experiment and meeting, we are resuming CASP ROLL with two new targets later this week. We made changes to our target submission system so that every time a new CASP ROLL target is posted for prediction - a message is sent to the registered group leaders. This way you should be able to better track appearance of new targets in CASP ROLL.

Also, for those of you who did not make it to Gaeta, we posted all assessors' presentations and some of the keynote talks on the web. Enjoy!

CASP organizers
Predictors meeting in Gaeta (2012-12-7)
Dear CASP10 Participants,

On the last day of the Meeting we will have our regular Predictors get-together. In advance, I would like to ask you to send in any comments regarding the CASP process in general and the operations of the Prediction Center in particular, as well as to share any additional insights you may have.

We would also like to return to the issue of making our collective efforts more relevant to the biology community. In what way could we make our network more helpful in advising on and/or guiding the modeling process? Would you be willing to get involved?

Please direct your comments to kfidelis@ucdavis.edu

Hope to see you all very soon in Gaeta,

Krzysztof Fidelis
for CASP organizes
Release of CASP10 results(2012-12-5)
Dear CASP10 Predictors,

We have released results of the CASP10 and CASP ROLL experiments. You can check now interactive results tables and graphs, as well as the parsable data, including the text SUMMARY_TABLES. As you will have noticed, coordinates for two non-canceled targets (T0695 and T0739) are still under the lock according to the requests of their authors.

In the last minute preparations for the meeting, we recommend that you download the CASP10 Abstract book and the text version of the automatic evaluation files to the laptop you take with you to the meeting, as we do not include CDs with these materials in your registration package. Don't be scared with this warning - the hotel in Gaeta does have wireless Internet, but we can not guarantee it will hold the load of 150 bioinformaticians simultaneously browsing the online results.

There were also minor changes in the program of the meeting - please check the website for the latest version.

Thank you and see you in Gaeta,
CASP10 organizers
CASP10 program; last week of registration(2012-11-26)
Dear CASPers,

We are in the final stages of preparation for the CASP10 meeting in Gaeta. All the speakers have been invited and the program has crystallized. We have a lineup of outstanding speakers, in particular:

Keynote talks:
Janet Thornton - Predicting structure and function: from dreams to reality.
David Jones - The impact of evolutionary information on protein structure prediction: past, present and future.
Michael Levitt - Two decades of CASP: the future of modeling and prediction in structural biology.
Manfred Sippl - Who solved the folding problem?
Roland Dunbrack - Structural bioinformatics for protein structure prediction.
Joel Sussman - Disorder - past, present and future.
Nick Grishin - Predictive landscape of CASP.
David Baker - From protein structure modeling to protein design.

Assessors talks:
BK Lee - Free modeling, CASP Roll and contact-assisted assessment
Gaetano Montelione - Template-based assessment
David Jones - Refinement assessment

Best predictors talks:
Yang Zhang - TBM and FM
Jooyoung Lee - TBM
Chen Keasar - FM
Michael Feig - Refinement
Baker group - Contact-assisted prediction
Hongyj Zhou - Model quality assessment

Methods talks:
David Jones - PSICOV
George Khoury /Gaurav Chopra - WeFold
Chris Sander - EVFold
Firas Khatib - FoldIt
Jinbo Xu - Raptor
Andrzej Kloczkowski - Kloczkowski_lab

Besides these talks we will also have a job fair, roundtables, poster presentations and more. The detailed program of the meeting is available from the main CASP10 web page (http://predictioncenter.org/casp10/doc/CASP10_Meeting_Program.html). Please note that we still have a few places for the conference available, but this week is your last chance to register as we are closing the meeting registration on December 1 and will not have an onsite registration option in Gaeta.

See you in Gaeta soon,

CASP10 organizers
End of Methods Talks voting; talk invitations; Gaeta ride sharing(2012-11-16)
Dear CASP Participants,

1. Voting on methods is about to conclude. The voting facility http://predictioncenter.org/casp9/voting.cgi will be open only until the coming Monday, Nov. 19. So if you have not done so yet, please vote today or over the weekend. More than 400 opinions have been already recorded and we can already see several methods that are leading the popular vote. Please note that you will be able to see the voting summary after you cast your vote.

2. We will be sending out invitations to the best CASP10 predictors (assessor-nominated speakers) and your selected methods speakers next week. The program of the meeting will be available shortly after the finalizing the list of speakers.

3. Those coming to Gaeta have probably checked our web page *How tp reach Gaeta*
(http://predictioncenter.org/casp10/meeting_directions.cgi)
for advises on how to get to the meeting venue. Please note that if you are leaning towards choosing the shuttle option for direct transportation from a Rome airport directly to the hotel, you can try to arrange for a ride sharing. To help you with this, we have opened a topic *Ride sharing for Gaeta* at the ForCASP forum http://predictioncenter.org/forcasp/.

CASP organizers
Voting for the Methods Talks starts(2012-11-9)
Dear CASPers,

This message announces start of the voting on the Methods Talks. Please cast your votes for the methods you consider worth presenting at the meeting at http://predictioncenter.org/casp10/voting.cgi. For your convenience, we compiled a book of selected abstracts that contains communications just from the nominated groups (http://predictioncenter.org/casp10/doc/CASP10_Abstracts_selected.pdf).

The voting facility will be open until Monday, Nov. 19. You should be able to track the voting summary after you cast your vote(s). In the past we noticed a positive correlation between the method(s) supported and vote's geographical origin, so please refrain from voting for your own method or that of your close collaborators as we will be filtering out such votes.

Authors of the methods that fared the most interesting for the community will be invited to talk shortly after the voting closes.

CASP Organizers
End of Methods Talks nominations - tomorrow(2012-11-8)
Dear CASP participants,

This is a reminder that tomorrow we will post the final list of candidates for the Methods talks voting.
If you want to nominate someone - please do it asap. Methods abstracts are available at
predictioncenter.org/casp10/doc/CASP10_Abstracts.pdf.

We also recommend saving the Abstract book to your laptop as we will not be distributing CDs with
abstracts and results at the meeting. Text tables with the evaluation results will be available through
our website in the first week of December.

CASP Organizers
Nominating abstracts for voting; poster size(2012-11-7)
Dear CASPers,

Many CASP participants communicated to the organizers that the Methods Session at the CASP9 meeting was very useful and informative as the presenters concentrated on the details of their methods rather than their performance in the experiment. Following on that success, we are planning to have another Methods session at the coming CASP meeting where people with interesting methods will be able to share details of their work.

The assessors have compiled an extended list of groups that performed not necessarily best but at least relatively well at this CASP. and we will suggest these lists for the Methods talks voting the coming Friday. But before we do that, we ask you to browse the abstracts yourself and nominate those methods you consider innovative, having potential to improve the field, or otherwise interesting for inclusion in the voting lists. Please send us an email with your nominee(s). The organizers then will compare the lists and suggest you a coordinated list for voting.

Please note that in addition to this there will be a different session where people with the most interesting posters (as determined by a special jury) will be asked to give short presentations. Therefore we ask all poster presenters to be ready to give a short talk at the meeting. By the way - the maximum poster size is 70x100 cm. If you have not registered to bring a poster but still would like to do so, please let us know immediately.

CASP Organizers
CASP10 job fair(2012-11-3)
Dear CASPers,

As in CASP8 and CASP9, we would like to take advantage of the CASP10 meeting to help young scientists looking for a position in Computational Biology and potential group leaders to meet there.

We plan to have time set aside to get them together for interviews / informal meetings /etc.

If you are looking for a position, could you please send your cv to anna.tramontano@uniroma1.it by the 15th of November?
If you have positions available could you please send a mail with the advert (or a short description in any case) to anna.tramontano@uniroma1.it by the 15th of November?

PLEASE USE THE SUBJECT "CASP10 JOB FAIR" in your email.

As soon as we have an idea of how many people are interested in this initiative, we will get back to you with more information.

Thank you very much.
The CASP organizers
CASP ROLL - new targets(2012-10-8)
Dear CASP ROLL participants,

After the post-CASP10 break we are resuming releasing targets for the rolling experiment. At the moment we have seven new targets, which will be gradually released starting tomorrow (2-3 targets per week). These targets will constitute a part of a new post-CASP10 cycle of the ROLL experiment.

CASP organizers
Sep.6 - early bird registration deadline; CASP fellowships letters(2012-9-4)
Dear CASP participants,

All recipients of CASP student fellowships have been identified and notified.
Please proceed with the registrations according to the instructions provided
in the award letters.

Also, please be reminded that the CASP early bird registration ends in two days.

CASP organizers
Abstract collection; meeting fellowships; early bird registration (2012-8-21)
1. Just three days ago we received the last CASP10 prediction, and today we start collecting methods abstracts. The Abstract Submission web page is available through a link from the CASP10 main page. Please read the instructions carefully and address all the questions in the form in your abstracts. The submission deadline is September 28th, 2012. Please remember that your contributions will be taken into account in choosing presentations for the meeting.

2. We would also like to remind you that this Friday, August 24th, we will stop accepting applications from students /minorities for financial support to attend the CASP meeting. Requirements for submitting the applications are available at the meeting registration page. All fellowship recipients will be notified by August 31.

3. If you want to take advantage of the discounted registration rates for the meeting - please act quickly as the "early bird" rates are in effect only until September 6th.

CASP organizers
End of CASP10 regular prediction; one last refinement target tomorrow(2012-8-2)
Yesterday we closed prediction for the last regular CASP10 target. The final CASP10 target statistics: 114 targets including 53 all-group targets. We expect the majority of CASP10 structures to be gradually released by the PDB in the next 5 weeks. We will be updating our target list weekly (on Wednesdays).

Tomorrow we will release the last target in CASP10 refinement experiment. With its release we will have 28 refinement targets, which is exactly twice as many as we had in CASP9.

There will be no more contact-guided targets in CASP10. All in all we were able to suggest you 15 targets in this new prediction category.

Thanks to all of you who made CASP10 yet another successful protein structure prediction experiment. Due to your dedication and the hard work we already received almost 65,000 predictions. Now it's time for the Prediction Center and the assessors' teams to evaluate them. We'll keep you posted...

CASP organizers
CASP10 meeting registration is now open(2012-7-31)
Dear CASP Participants,

The early bird registration for the CASP10 Meeting in Gaeta, Italy (Dec. 9-12, 2012) is now open via the UC Davis Conference and Event Services. The link to the registration form is available at http://www.predictioncenter.org/casp10.

CASP Organizers
Last CASP10 regular target has been released(2012-7-17)
Dear predictors,

Good news: we have released our last regular target today, reaching 114 targets, including 53 all-group targets, for the season. With the re-organization of the Structural Genomics centers, it was not an easy year to provide targets but in the end we reached the numbers we have planned. We would like to take this opportunity and acknowledge the crystallographers and NMR spectroscopists who participated. The main share of targets was again obtained from the Structural Genomics centers, and we want to thank them for their continuous support of CASP, especially the JCSG, which provided almost 40% of all CASP10 targets (see http://predictioncenter.org/casp10/numbers.cgi). We also want to emphasize that almost 20% of the targets this season came from the non-SGI research groups, almost twice as many as two years ago.

We will continue pushing tasks to the QA servers until the last server target expires and releasing refinement and contact-assisted targets until the end of the month. By the end of this week we plan to release at least 3 more refinement targets.

Based on the availability, we will also continue releasing challenging targets for testing free modeling methods to those groups that participate in the rolling CASP experiment. For your convenience, we will be sending alerts to CASP ROLL participants when new targets are released.

CASP Organizers
CASP10: week 11 update(2012-7-10)
Dear predictors,

1. CASP10 target release season is entering its final stage. We plan to release last regular all-group target tomorrow (July 11). We will continue releasing server-only targets through next Tuesday (July 17). If we receive a difficult target during the final release week, we will squeeze it into the schedule (with a slightly shorter than usual deadline) and notify you via the newsletter. After July 17 we will be releasing only refinement and contact-assisted targets.

2. We just learned that a copy-and-paste mistake encroached in the sequence of target T0725. You can notice two pseudo-repeat units there that in fact are not present in the native sequence. For the cleanness of the prediction experiment, we are canceling target T0725 and re-releasing the corrected sequence as a new target T0745. This target has been solved as a dimer.

CASP organizers
CASP10: week 9 update(2012-6-28)
Dear predictors,

We are finishing 9th week of CASP10 target release and are on track of having 100+ targets total, including 50+ 'all group' targets. As we approach the last two weeks of target release we ask you to make the last push in getting interesting targets for our experiment by contacting your experimental colleagues and asking them to submit potential targets to CASP right away.

We are also moving forward with refinement and contact-assisted targets, having ten of each already released. Please remember that we will continue releasing these targets through the whole month of July.

Next week there will be no targets on Wednesday, July 4.

CASP organizers
T0690 - long deadline target(2012-6-9)
Dear predictors,

We have reasons to believe that target T0690, which was originally released as a server-only target, is more difficult for prediction than originally thought. Therefore we move this target to the all-group category and extend its manual group prediction deadline by June 22.

CASP organizers
CASP10: week 6 update(2012-6-8)
Dear predictors,

We have crossed the equator in CASP10 target release. Seventy-one targets have been released, including 65 regular, 1 contact-assisted and 5 refinement targets. Next week we plan to release 3-4 new targets for contact-assisted prediction. We have evaluated results for the first CASP ROLL contact-assisted predictions and learned that releasing 4-5 contacts per target did not help much predictors in modeling. Therefore in CASP10 we will be releasing more contacts. We plan to release L/15 - L/10 contacts per target, where L is the target length. Please remember that we release not the contacts that are the most popular, but vice versa - the contacts (mainly long-range) that are important for folding but were missed by the vast majority of predictors. Contact information is provided in the "Additional Information" section of the target page and also posted as a separate file at http://predictioncenter.org/download_area/CASP10/extra_experiments/ .

Please also note that deadline for one of the CASP10 targets - T0678 - has been moved one day ahead, to June 10, as this target (4epz) is to be released by the PDB on June 11.

CASP organizers
CASP10: week 4 update(2012-5-24)
Dear predictors,

You might have noticed that the recently released target T0682 is too easy for inclusion in the all-group target set. This target, however, is quite unusual for modeling. Looking at it more closely, you will easily find a closely related template for homology modeling, but be aware that its structure has substantial structural errors. Relying only on that template would likely give you less than satisfactory results. We see this target as an exercise in homology modeling based on a structurally poor template + subsequent refinement. So, if you plan to participate in the refinement experiment, please send your predictions for this target as a regular submission. First normal CASP10 refinement targets are planned to be released within the next few days.

Next week we will be releasing targets as usually, starting on Monday.

CASP organizers
CASP10: week 3 update(2012-5-16)
Dear predictors,

You might have noticed that we have released a couple of challenging targets this week. We will have a few more by the end of this week.

We also wanted to let you know that these days the organizers, old CASP9 assessors and new CASP10 assessors are having a planning meeting. The future TBM assessor has brought up the issue of model completeness, specifically that the prediction field has matured to the point where we should be requesting that all backbone and side chain atoms are present and reasonably packed in the submitted template-based models. We will still accept incomplete models but we would like to let you know that in this round of CASP the C-alpha or backbone only models (TBM) may (and likely will) be penalized in the assessment. Also, the TBM assessor would like to encourage predictors to submit oligomeric models wherever possible.

CASP organizers
CASP10 - week 1; appeal for targets(2012-5-2)
Dear predictors,

CASP10 is already off and running and we are anticipating another exiting prediction season! We have released five targets in the first two days of the experiment, and plan to release four more by the end of the week. To start it gently, we will be releasing only relatively easy template-based modeling targets this week. The more difficult targets will be released starting next week.

Thanks to the Structural Genomics centers, we currently have a supply of targets large enough to run the first three weeks of prediction, at a 12 targets/week load. However, because of the shift of the big SG centers away from coverage of structure space, the majority of these structures appeared to be template-based and just 3 or 4 of them vaguely fall to the free modeling category. In CASP9, a substantial share of more difficult targets came from experimental groups outside the SGI centers, and we very much need your help this time again to contact the broader structural community with an appeal for targets. We need all sorts of targets but most of all:
* novel folds and membrane protein targets;
* template-based modeling targets with lower sequence identity to template, right down to undetectable;
* targets containing significant amounts of disordered structure.

One mechanism that worked well in previous CASPs: each prediction group beats the experimental bushes to find at least one target. Personal approaches work MUCH better than mass e-mailings. What we are asking is that you each approach at least one, more if possible, experimentalists, and make a direct, strong, personal plea that they provide a target, explaining why it is important. Please direct them to the target submission URL for details of the process: http://www.predictioncenter.org/casp10/targets_submission.cgi

OK, that's about it. Please get in touch if you have any questions or concerns.

Hoping for lots of targets,
CASP organizers
May 1 - first CASP10 targets; new CASP ROLL contact-guided targets(2012-4-26)
Dear CASPers,

We are in the last stages of preparation for the opening of the anniversary CASP season. The first CASP10 targets will be released next Tuesday, May 1. As of today, over 200 predictor groups have registered for CASP10; if you are planning to participate but have not registered yet - please do this as soon as you can. Even if you are a veteran CASP participant, we encourage you to reread the CASP10 format page, as the email address for submitting predictions has changed as well as the rules for submitting QA estimates. Also, now is about the last chance for server curators to resolve any remaining issues with connectivity of their servers to CASP distribution/ verification servers.

For those participating in CASP ROLL, we want to bring your attention to the fact that we released 3 structure-guided prediction targets during the last two days.

CASP organizers
Server dry run - third round on April 23(2012-4-20)
Dear CASP10 participants,

We are happy to announce that the second round of testing servers is over and we were able to get practically all of the currently registered 87 servers properly connected and returning predictions in the correct format. There are still a few servers that either are not online yet or do not accept the parameters that our distribution server is sending to them. If you have not received a request from us or have not seen confirmation/rejection messages from our verification system - it should be something wrong with your connectivity or the parameters specified at the registration. Please get back to us as soon as you can to remedy the situation. We will be having our last round of servers dry testing next Monday.

CASP organizers
CASP10 dry run for servers(2012-4-16)
Dear Caspers,

As of today, 72 prediction servers have been registered for CASP10 experiment. We have started checking connectivity and correctness of prediction format for the servers in non-QA prediction categories. We have sent them 1-3 requests to predict the test target T0921. If you had registered a TS, RR, DR or FN server, but have not received at least one request from us - please check your registration settings and contact us if in doubt. Quality assessment servers will be tested starting tomorrow afternoon (PST). We also plan to send one more modeling request to all registered non-QA servers tomorrow morning (PST). So, if you plan to participate in the server track but have not registered your server(s) yet - we advise you to do so immediately. During the tomorrow tests you will be receiving both, acceptance and rejection messages from our verification server. During the regular season, though, acceptance messages will be suppressed.

A request to all EMAIL-server curators: please, make sure that your servers reply to our distribution server casp-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0921 - query received by MY_SERVER". Failing to do this will not prevent you from participation in CASP10 but will affect the timely addressing of unexpected connectivity failures. The prediction itself should be sent to the address specified in the field REPLY-E-MAIL of the query (please note that this address should be always taken from our query and not hard-coded as we may change it during the season).

CASP organizers
CASP ROLL - target update; CASP10 - registration continues(2012-3-30)
Today we have released our fifth special interest CASP ROLL target (Rc012). We are able to offer you 3 full weeks for the contact-assisted prediction of R0012. Information about the domain delineation and some contacts in this target is posted to the Rc012 target page.

---
CASP10 registration continues with 120 groups already registered. If you plan to register a server for participation in CASP10, we ask you to do so at your earliest convenience as this will allow us some extra time to check the readiness of your server.

CASP organizers
CASP10 - registration(2012-3-28)
The registration for CASP10 experiment is now open. The link to the registration pages is available from the CASP10 main page: http://predictioncenter.org/casp10. The page also provides description of the experiment. Please read through as some of the rules have changed compared to CASP9, in particular, those pertaining to the release of server predictions and QA submission procedures. Detailed information on CASP10 prediction submission procedures and format is available from our format page: http://predictioncenter.org/casp10/index.cgi?page=format .

For convenience of the predictors who are currently participating in CASP ROLL, they have been enrolled also in CASP10 with the same group id, group name and PIN number. The current CASP ROLL participants should now be able to access their CASP10 registration data and make updates if necessary. Please note that by using this pre-registration procedure your group name can not be changed for CASP10; if this is imperative for you - you will have to register a new group with the desired name and inform us that you don't want your CASP ROLL group enrolled in CASP10. We have changed the CASP acceptance system so that the predictors participating in both experiments can submit their predictions for the targets selected for both experiments only once (to CASP10).

If you have any questions concerning the registration - please send them to our casp at predictioncenter account.

CASP organizers
Slightly shorter deadlines for R0012 and Rc007; CASP10 registration - March 28. (2012-3-24)
CASP ROLL.

We are reducing by a couple of days the prediction period for two of the CASP ROLL targets:
R0012: old deadline - March 30; new deadline - March 29
Rc007: old deadline - April 2; new deadline - March 30.

*****
CASP10.

We will be opening CASP10 registration on Wednesday, March 28.

*****
CASP10 - CASP ROLL compatibility issues.

As we have already announced, during the regular CASP10 prediction season (May-July) both experiments (CASP10 and CASP ROLL) would run in parallel. For convenience of the predictors who are currently participating in CASP ROLL, we will automatically enroll them in CASP10 with the same group id, group name and PIN number. This way we try to avoid confusion of your having two different group IDs and PIN numbers in the two experiments. If you are currently participating in CASP ROLL but do not plan to take part in CASP10 - please send us a message and we will skip your automatic CASP10 enrollment. After the automatic registration, the current CASP ROLL participants will be able to access their registration data and make updates if necessary (e.g., add information that a server already enrolled in CASP ROLL will also be sending QA or DR predictions in CASP10). Please note that you will not be allowed to change your group name for CASP10; if this is imperative for you - you will have to register a new group with the desired name in CASP10 and inform us that you don't want your CASP ROLL group enrolled in CASP10. In this case you would have to handle submissions separately for the groups registered for both experiments: we are currently changing the CASP system to allow sending predictions only once for the targets selected to both experiments.

CASP organizers
Halting automatic queries to servers for contact-assisted prediction(2012-3-14)
Dear CASP ROLL participants,

Yesterday we have polled the CASP ROLL server curators about the readiness of their servers for contact-assisted prediction. Based on their response, we conclude that the vast majority of servers do not have yet the functionality to automatically utilize provided contact information. Therefore, we will stop sending queries in this category to all servers. Please send us a message when your server is ready for contact-assisted prediction and we will resume sending automatic requests to your server(s).


Target update.

Today we have released our third target for contact-assisted prediction (Rc001). Please note that the deadline for re-prediction is 2-weeks.

Tomorrow we will release our 16th regular CASP ROLL target.

On Friday we will release the first target for the chemical shift (CS) guided prediction of an NMR structure (Rs003). Chemical shift information will be provided in a separate file (BMRB format) available for download from the predictioncenter.org/download_area/CASPROL/extra_experiments/ page. As with the contact-assisted prediction, we will NOT be sending queries to the CASP ROLL servers for the CS-guided targets unless you request us to do so.


CASP organizers
Contact-guided structure prediction in CASP ROLL(2012-3-9)
Dear CASPers,

The CASP ROLL experiment is in full swing with more than 50 groups contributing. With the release of today's target we are at the 15-target mark. CASP ROLL registration is still open and it is not too late to join the experiment.

We have recently polled the community concerning interest in the additional structure-guided prediction experiments (contact-guided structure prediction, chemical shifts-guided modeling of NMR structures and structure modeling based on molecular replacement using ab initio models and crystallographic diffraction data). The biggest interest was expressed for the contact-guided structure prediction. Therefore, we are going forward with this initiative next Monday. We will be releasing 3 to 5 long-range contacts for some of the more challenging targets, provided we can get coordinates in advance and have enough time (at least 2 weeks) for re-prediction. The definition of residues in contact will be the one used in CASP contact prediction category: 8A distance between C-beta atoms (or C-alpha for glycine). For release, we will select contacts based on the specifics of fold and the success in prediction of particular contacts. Priority will be given to contacts important for correct protein folding and those where fewer than 10% of predictors were able to identify them.

Targets will be called based on the name of the original target. For example, the target for contact-guided prediction of the regular CASP ROLL target R0010 will be called Rc010 (notice the small letter 'c' in target's name). Information about the new targets will be made available through the main experiment Target List page. Contact information will be provided at the target-specific pages under the Additional Information section and also as a separate file available for download from the predictioncenter.org/download_area/CASPROL/extra_experiments/ page. Format for releasing contacts will be as follows:

REMARK Rc010: CONTACT-GUIDED STRUCTURE PREDICTION
CONTACT_1: 167A:25C
CONTACT_2: 116L:77K
...

Predictions should be submitted according to the rules of the corresponding main experiment, i.e. for targets originating from the CASP_ROLL experiment, predictions should be sent using the CASP ROLL web submission form or by sending an email to the casprol account.

If you do not currently participate in CASP ROLL but would like to participate in contact-guided structure prediction, you should register for CASP ROLL first and then send us predictions using the assigned CASP ROLL group code.

We look forward to a successful contact-guided prediction experiment next week!

CASP organizers
Changes for CASP10 quality assessment category(2012-2-22)
Dear prospective CASP10 participants,

We have posted at the FORCASP site the suggested changes to the CASP10 QA prediction and evaluation procedures. Please follow this link to read the details:
http://predictioncenter.org/forcasp/viewtopic.php?f=24&t=463&sid=b451a5971d4596ba29a5d53d213bdc52

CASP organizers
Collaborative group initiative(2012-2-14)
Dear member of CASP community,

Silvia Crivelli (LBNL, UC Davis, and a member of this community since 1998) is organizing a collaborative group to participate in CASP10 and possibly in CASP ROLL if time permits. This collaborative experiment will let different groups or individuals work on different components of the protein structure prediction pipeline (like alignment, loop modeling, scoring, etc) thus making it possible to leverage expertise at a large scale. The initial goal is to focus on ab initio targets. Certain groups may want to participate in the collaborative effort for all the ab initio targets while others may want to do just a few of them.

If you would like to learn more about this effort please visit wefold.wordpress.com or contact Silvia directly at SNCrivelli@lbl.gov.
Extra CASP experiments(2012-2-1)
At the most recent CASP meeting, members of the modeling community suggested launching several additional experiments that would benefit developers of predictive methods. We have successfully started one of the suggested initiatives - Rolling CASP - for modeling of difficult FM targets. The first CASP ROLL targets are now reaching their deadlines, and we are considering further experiments with some of them. The purpose of this email is to determine which experiments there is sufficient interest in.

Please let us know which of the following you expect you would take part in:

1. Chemical shifts guided modeling of NMR structures.

2. Structure modeling based on molecular replacement with ab initio models and crystallographic diffraction data.

3. Structure modeling knowing a few (1-3: how many?) important long-range contacts, either randomly selected or based on possible results from lysine crosslinking experiments (please indicate whether one of both would be of interest).

CASP organizers
CASP ROLL targets(2011-12-2)
The second CASP ROLL target will be released next Monday, December 5, 2011.
Rolling CASP experiment - Start(2011-11-30)
Dear Caspers,

This is the last call to register for the CASP ROLL experiment in time for the first target release. We are pleased to announce that 40+ groups, including 20 servers, have already registered for the experiment. We have run connectivity checks for all of the registered servers and the majority is ready to begin. If you still have problems with your registered server(s) or are planning on registering new ones today - we will be continuing debugging server issues starting at 8 am PST today, November 30. If you experience any problems with your server(s) please let us know ASAP.

All CASP ROLL targets will have 3-day deadline for server predictions and at least 3-week deadline for regular group predictions. If possible, we will set more distant deadlines for regular group predictions so that physics-based groups get more time for running their methods. Please be aware, though, that in the unlikely situation when a target is publicly exposed before the regular deadline (and after the 3-week soft deadline), only models received within the initial 3-week prediction window will be considered. Therefore we recommend submitting the best models you obtain within the 3-week prediction period first, and then resubmitting the final models before the regular deadline.

The first target will be released tomorrow, December 1, at 9 am PST and will have a 10-week regular (non-server) deadline. There is a good chance that we will have another target for release on December 2, and a couple more - the following week. We will send an appropriate message to the registered CASP ROLL participants.

Good luck!
CASP organizers
Rolling CASP experiment - Registration(2011-11-23)
We are opening registration for CASP ROLL experiment.

To register for the experiment, you will have to login to your Prediction Center (PC) account first (or register if you haven't done this before) and then go to the CASP ROLL web page and choose one of the five registration forms available there. Please, read the registration instructions to choose the appropriate form.

We ask that you register for the experiment at your earliest opportunity as we will be testing the connectivity with the registered CASP ROLL servers without any delay. We have already two targets at hand and are planning on releasing them for prediction on December 1, as it was announced earlier.

CASP organizers
Rolling CASP experiment(2011-11-2)
Dear CASP participants,

According to the suggestions of the CASP9 predictor meeting, we are announcing the Rolling CASP experiment.
Please follow the appropriate link from the Prediction Center main page http://predictioncenter.org/ for details.

We are also glad to inform you that there will be a regular CASP10 experiment in Spring-Summer of 2012 with the predictor meeting in December 2012 in Italy.

CASP organizers
A new local model quality visualization tool is now available(2010-12-2)
Dear CASP9 Predictors,

The current distribution of the CASP evaluation results which was just released comprises a new powerful local model quality visualization tool called the SphereGrinder, worth perhaps a few words of introduction.

The new approach is based on multiple local superpositions rather than a single global superposition or a series of global superpositions (as in GDT_TS). This avoids a possible shift error in some parts of the model. The general idea is to calculate RMSD inside a sphere centered on each amino acid in the target structure, i.e. to identify the atoms inside the sphere and calculate the superposition with the corresponding atoms of the model. In the visualization modes, a series of sphere radii are used for which the corresponding RMSDs are reported. Thus in one glance it is possible to assess the local accuracy of an entire model.

Another aim of developing this approach was to facilitate identification of any reasonable models submitted on FM targets. To this end models may be ranked by the number of residues for which the local structure does not deviate from target by more than a user defined RMSD cutoff. This particular option is available in the Cutoff mode.

The SphereGrinder (SG) is Java based and can be launched from the standard target pictogram: http://www.predictioncenter.org/casp9/results.cgi . A help file is available from inside the SG viewer. Please let us know if you have any suggestions on how to further improve this tool.
Fourth UCSC/QB3 Symposium on Bioinformatics - FREE!!(2010-11-22)
Fourth UCSC/QB3 Symposium on Bioinformatics
FREE!!

Engineering Auditorium
University of California, Santa Cruz
10-11 Dec 2010

As of 22 Nov 2010, we have only 3 abstracts and 21 registered attendees. I need at least 3 more abstracts to do a one-day conference (and 8-9 more for the originally planned 2-day conference). The speakers whose abstracts I have are Thomas Huber, Oscar Westesson, and Manel Camps. Three others have indicated a willingness to speak, but not sent me titles or abstracts. If they all follow through, I'll have enough for a one-day conference, but I'd really like 6 more speakers.

I also need at least 10 more attendees to register to make it worthwhile holding the meeting. The deadline for my decision on whether to hold the meeting or cancel it due to lack of interest is this weekend, so please send me your abstracts and register by Nov 24!

Kevin Karplus


Here is the original announcement:

All bioinformatics researchers and students are welcome to attend our free symposium. We would particularly like to invite all the attendees of CASP9 to stay on the Central Coast an extra couple of days for informal talks at UCSC.

The symposium is Friday Dec 10 and Saturday Dec 11. Researchers (primarily attendees of the CASP9 conference on prediction of protein structure, but also other bioinformatics researchers who are in the neighborhood) are invited to present any interesting work they have done recently as 40-minute talks (40 minutes plus 5 minutes for questions). Ideally, speakers will be talking about something different from any presentation they might give at CASP9. By scheduling the symposium after CASP there will be no "scooping" of CASP results.

There will be no refereeing of papers, no proceedings, and no money involved. We won't be arranging hotels, fancy meals, or any of the other things that can complicate running a conference. (It is the off-season for Santa Cruz hotels, so finding a reasonably-priced room should not be hard.) You can also search Google for Santa Cruz hotels.

QB3 (the California Institute for Quantitative Biosciences) has agreed to sponsor the coffee breaks and lunches at the symposium. In order for them to do this, we need fairly accurate counts of how many people will be attending. To this end we are asking that people who are coming register by Nov 24th using the form we have set up at pingg.

http://www.pingg.com/rsvp/f3xys5dp6573e88ng

Our reason for holding this conference is to get a bunch of interesting speakers to talk at UCSC. The incentive for others is an excuse to stay a little longer in California, and perhaps to talk about some more speculative work that isn't ready for archival conference or journal publication. Presenting material that has already been published but deserves wider dissemination is also very welcome.

Speakers are scheduled on a first-come-first-served basis (more or less). Prospective speakers should contact Kevin Karplus (karplus@soe.ucsc.edu ) and let him know

* your name and contact info
* your title and short abstract
* whether you can talk Friday, Saturday, or either.

This announcement can be found at
http://compbio.soe.ucsc.edu/workshop-2010.html
along with information about getting to UCSC and links to the
registration form.

Voting on the abstracts(2010-11-18)
Dear CASP Participants,

Voting on methods is about to conclude. The voting facility http://predictioncenter.org/casp9/voting.cgi will be open only until Monday, Nov. 22. So if you have not done so yet, please vote soon. Over 400 opinions have been recorded so far. Please note that you can see the voting summary after you cast your votes.

We also want to warn you that we are noticing a positive method /vote geographical origin correlation. So please try to refrain from supporting your own work more than once ;-)


CASP Organizers
Student /Postdoc input to CASP(2010-11-15)
Dear CASP Students /Postdocs

The CASP meeting is rapidly approaching. We will accept your input regarding the following until the end of this week.

1. About CASP in general: Are there any suggestions you would like to make regarding CASP sessions and particular topics you would like to see discussed.

2. About Student /Postdoc session in particular. Here Gaurav Chopra has prepared a special input web page. Please go to https://spreadsheets.google.com/viewform?formkey=dG0wbFY0aDA4SkI5TzZfLTRwRDljQ3c6MQ and send us your input.


Krzysztof Fidelis
for CASP Organizers
Voting on the abstracts(2010-11-15)
Dear CASP Participants,

We are planning to have a special Methods session at the coming CASP meeting where people with new/improved/interesting methods will share details of their work.

The assessors have compiled an extended list of groups that performed not necessarily best but at least relatively well at this CASP. We suggest that you check abstracts from these groups (http://predictioncenter.org/casp9/doc/Abstracts_selected.pdf) and select methods you consider innovative, having potential to improve the field, or otherwise interesting. Please cast your votes for these methods at http://predictioncenter.org/casp9/voting.cgi .

Please note that this will be a different session than the "Highlights" one, for which the speakers will be selected by the organizing committee based on recently published papers (see the recent announcement at our web site).

CASP Organizers
Influence future directions(2010-11-11)
Dear CASP Participants,

Since the first meeting in 1994, CASP has evolved considerably, including introducing new prediction categories, improving assessment techniques, and changing emphases of discussions during the meeting. To stay on track we ask you to look ahead, and help us correct things that do not quite work and recommend changes that would make CASP better. Therefore we request that you send us your suggestions in the next week.

We hope that your input will spawn a special session during the Asilomar meeting, including short individual presentations and discussion. Please write to Krzysztof Fidelis, kfidelis@ucdavis.edu, with specific suggestions.

We would also like to see this kind of issues discussed on the FORCASP forum in advance of the meeting.

Krzysztof Fidelis
for CASP Organizers
Posters at CASP(2010-11-11)
Dear CASP participants,

The maximum poster size will be 41 (Height) x 47 (Width) inches [1 inch = 2.54 cm]. If you have not registered to bring a poster but still would like to do so, please let us know immediately.

CASP Organizers
Student /Postdoc session at CASP (2010-11-11)
Hello CASP Students and Postdocs,

We are all excited about the CASP9 meeting in December. The CASP organizers want to present the students and postdocs with a unique opportunity where we can get the most out of the CASP meeting. We ask you to give inputs about making different sessions at CASP better in terms of what you think each session should discuss and how it should be presented. Please send us your suggestions!

Moreover, this year we are organizing a "Student Session" at CASP, which would be a perfect stage to ask questions to the leaders of the structure prediction community.

We ask for volunteers to help with the following to make the student session a success:

1. What would you like to see at this session - a Q&A session with panel of successful predictors, specific presentations etc. Please think about this in way so that you can benefit the most from this session.

2. Specifically, what questions would you want to get answered. It would be great to see a list of questions related to structure prediction and its applications or about the future of CASP and what is missing in the current successful methodologies.

3. Would you like a poster session at CASP, where the 10 best posters are picked to present a short talk (5 minutes each).

4. One predictor who you really want to see on the Q&A panel or give a specific presentation and WHY?

These are just a few ideas. It would be great to get more from all of you.

If you would like to volunteer to organize this session, please let us know by emailing us.

Best Regards,
Gaurav Chopra (gauravc@stanford.edu)
Krzysztof Fidelis (kfidelis@ucdavis.edu)
(2010-11-8)
Dear CASPers,

We would like to introduce a new "highlight" session at CASP where published work relevant to our field will be presented.

To this end, we invite you to send us full papers that you have published, or that have been accepted for publication, in the last year and that are focused on biological/biomedical/biotechnological applications of protein structure prediction.

A committee will select the paper(s) to be presented at the meeting on the basis of their interest to the CASP audience, of the impact of the work on the field and on the likelihood that the work will make a good presentation.

We look forward to receive your submissions.

CASP Organizing committee
CASP9 job fair(2010-10-28)
Dear CASPers,

As in CASP8, we would like to take advantage of the CASP9 meeting to help young scientists looking for a position in Computational Biology meeting potential group leaders and vice versa. We plan to have time set aside to get them together for interviews / informal meetings /etc.

If you are looking for a position, could you please send your cv to anna.tramontano@uniroma1.it by the 12th of November?

If you have positions available could you please send a mail with the advert to anna.tramontano@uniroma1.it by the 12th of November?

As soon as we have an idea of how many people are interested in this initiative, we will get back to you with more information.

Thank you very much,
The CASP organizers
Additional funds covering registration costs may be available for students and post-docs(2010-10-14)
If you have already registered for the CASP meeting or are planning to register, and wish to be considered for the registration waiver - please send us your short CV, identifying yourself as a student or a post-doc.
Post-CASP workshop at UCSC - Dec. 10-11(2010-9-24)
We're going to have the post-CASP workshop at UCSC on Friday Dec 10 and Saturday Dec 11 2010.

Information at http://compbio.soe.ucsc.edu/workshop-2010.html

It is once again free (sponsored by UCSC and QB3) but we are asking people to register, so that the organizers can provide coffee breaks and (most likely) lunches.

A PINGG invitation system for people to register is available through the web page.

Kevin Karplus
Register for the CASP9 Meeting at Asilomar Now(2010-9-24)
Dear CASP Participant,

The Asilomar Meeting and Lodging Registration are now open at http://predictioncenter.org/casp9. Please note that the best Conference Registration rate (Early Bird) will only be available until October 3, 2010. Accommodation choices include the usual Asilomar room selections, i.e. Historic or Standard, and a selection of Single or Double occupancy (i.e. with a roommate). Accommodations are assigned on first come first served basis. Right now all selections are offered but please be aware that we may run out of the more popular choices or any on-site accommodation before the registration closes.

A limited number of registration/accommodation fellowships and a very limited number of travel fellowships will be available. However, registration and payment should not be made contingent on an accommodation or travel award. In case an award is granted, the registration fee, lodging fee, and/or travel costs will be reimbursed.

Please note that Financial Aid application deadline is October 3, 2010.

CASP Organizers
_______________________________________________________________

MEETING REGISTRATION

Meeting fees consist of a registration fee and a lodging fee for four nights (December 5-9, 2010) and have to be paid on line at the time of registration.

Registration Fee

Registration fee includes admission to all sessions, conference materials, coffee breaks, etc. The registration fees are as follows:

Early Bird Registration Special (AVAILABLE ONLY UNTIL October 3, 2010): $500
Regular Registration: $575
Late Registration (after October 22, 2010): $750

Lodging fee

Lodging fee includes hotel stay for four nights and all meals. The lodging fees are as follows:

Historic Room Double Occupancy: $424 (+ Registration fee)
Historic Room Single Occupancy: $628 (+ Registration fee)
Standard Room Double Occupancy: $488 (+ Registration fee)
Standard Room Single Occupancy: $796 (+ Registration fee)
Methods abstracts (2010-8-30)
Dear CASP9 predictors,

It's abstracts time! The Abstract submission web page is available through the link from the CASP9 main page. Please read the instructions before submitting your abstract as format requirements have changed. The submission deadline is September 20, 2010. Please remember that your contributions will be taken into account in choosing some presentations at the meeting. Also, the predictors presenting posters at the meeting should be prepared to give a short presentation at one of the main sessions as some talks will be invited during the meeting based on the discussion of poster sessions.

Short update on the CASP9 evaluation progress. At this moment, the Prediction Center team and assessors are working at full load evaluating your predictions. As of today, the PDB have released structures for 78 CASP9 targets. You can check which targets have been already released by the PDB from our target list page. We also have more than a dozen structures at hand received directly from the experimentalists. The preliminary evaluations have been run on all of these structures. The assessors are at the final stages of defining domains and categorizing the targets so that the final evaluations can be compiled.
End of the CASP9 prediction season(2010-7-30)
Tomorrow is the deadline for submitting predictions for the remaining 3 out of 4 human/server CASP targets (T0643 expires next week). The final CASP9 target statistics: 129 targets including 60 human/server targets. We expect the majority of CASP9 structures to be gradually released by the PDB in the next 5 weeks. We will be updating our target list weekly (on Wednesdays). As of today, thirty-nine CASP9 targets have already been released by the PDB.

Also, today we have released the last (and we believe the most challenging one) target for the refinement. The details of the suggested target are as usually provided in the "Additional information" field of the target page. All in all, we have released 14 targets for the refinement experiment in CASP9. This is two targets more than we had in CASP8.

Now it's a good time to thank to all of you who made CASP9 yet another successful protein structure prediction experiment. We have already received a record number of 85,000 (!) predictions from you this season, and still counting. Thanks to your dedication and the hard work! Now it's time for our computers at the Prediction Center and the assessors' teams to evaluate the predictions. We'll keep you posted...

CASP9 organizers

T0622 - additional information(2010-7-25)
T0622 expires for human prediction coming Tuesday. Those, who participate in the refinement experiment should have noticed the additional information we have posted about this target on the Refinement Target List page. We want to make sure that all the predictors are in equal conditions and noticed this info.
TR614 and TR622(2010-7-23)
We released two more refinement targets today. Please note that even though we suggested two different models as starting points for TR614 refinement, it is technically only one refinement target and only one structure
should be provided in the prediction (no residue repetitions).
Next week we will conclude the release of the refinement targets. Hoping for 2-3 more targets depending on structure availability and suitability of the models for the refinement.
T0637 - reverted to server only target(2010-7-21)
Target T0637 was independently solved by another crystallographic group and publicly released by the PDB today. We are reverting it back to the server only status.
July 17 - the last day of the target release (update - 2)(2010-7-17)
In the first two hours after releasing today's targets we have received a couple of requests to extend shorter than usual deadlines for the human/server targets released this week. We have discussed these requests and decided to slightly spill over into the first week of August in order to give you the full 3 weeks for prediction of T0637 and T0643.

CASP9 organizers
July 17 - the last day of the target release (update)(2010-7-17)
Just a few hours ago we received from our target depositors a sequence that shows no significant similarity to sequences of the PDB proteins. As hard prediction targets are getting more and more rare, it would be pity to waste such a good target. Therefore, in addition to the two server targets prepared for today's final release, we will be releasing another human/server target - T0643.

Sorry for the somewhat hectic last week of the target release season.
July 17 - the last day of the target release(2010-7-16)
Dear CASP9 participants,

As of today, July 16, we have released 126 targets for prediction including 61 in the human/server category. Please pay attention that the yesterday's target T0637 has been switched to the human/server category to compensate for the target reverted to the server only category yesterday. The last additions to the target list will be two more server targets that are scheduled for release tomorrow. And that would be it for regular prediction targets!

The CASP9 target statistics figures are well in accordance with the plan that we had for this round of CASP and very similar to the CASP8 figures (128/57). We wish to thank all the researches who were part of the CASP9 target collection effort, especially to the crystallographers and spectroscopists from the 3 Structural Genomics Centers (JCSG, NESG and MCSG), who provided more than 100 targets altogether for the CASP9 experiment.

We will continue pushing tasks to the QA servers until the last server target expires for prediction (July 21).

One more model was added to the refinement experiment today (TR606) and we expect to add a few more within the next two weeks.
T0555 is reverted to the server only targets(2010-7-15)
Yesterday we announced about moving T0555 to the human/server category. On the same day, unluckily for us, the PDB released structure of 2ky4, which is our another target - T0553 and a close homologue of T0555. Under these circumstances prediction of T0555 by human-expert groups is not that challenging any more (for those who update their structural libraries regularly, of course). Therefore, we return T0555 back to the server only status and no new predictions will be accepted on this target.
Switching T0555 and T0562 to human/server prediction category(2010-7-14)
Two more targets released in the "server only" prediction track, T0555 and T0562, appeared to be hard enough for modeling. We want to check if human-expert groups can do better on these targets and shifting them to the human/server prediction category. The human prediction deadlines for these targets are reset to July 31.
T0600 canceled for human predictions(2010-7-12)
We have canceled T0600 for human prediction as ribbon diagram of the structure had been prematurely exposed on the Internet. The target has been moved to the "server only" prediction category. Server predictions only will be assessed for this target.

Two more targets were released for the refinement today. We may potentially release one or two more later this week.
Week of July 12 - the last week of CASP9 target release(2010-7-9)
We have almost finished releasing human/server targets for prediction in CASP9. We are at the number 57 so far. This week we released more targets of this type than usual in order to give you full 3 weeks to predict each of them. Next week is the last, 11th week of CASP9 target release and we will be releasing predominantly "server only" targets (based on their availability) with a shorter human deadline for them. If something really, really interesting shows up during this last week and it will be pity to waste such a target for server only prediction - we may release it as a human/server target. There will be at least one such a target released next Monday, but not more than 3 of them for the whole week.
Another starting model for TR517 and new refinement targets(2010-6-28)
While predictors can use any of the server models as the starting model for the refinement, we advise you which models turn to be the best so that the refinement can work better for you. Last week we released TR517 for refinement selecting one of the best server models as the starting model. This model had some missing residues while the best human model had all the residues in place. We want to provide you this model as a potentially better starting point for the refinement. Please recheck the Refinement Target List page for the new starting model TR517.

We have also released 3 new refinement targets and are planning on releasing another one tomorrow.

CASP organizers
CASP9 update - June 25(2010-6-25)
Only three weeks are left for the release of targets this season. So, if someone knows a crystallographer or a NMR-spectroscopist who might have interesting targets for our experiment, please ask them to submit those to CASP right away.

This week we have released the first two targets for model refinement - TR517 and TR530
(http://predictioncenter.org/casp9/targetlist.cgi?view=refinement). The details of the suggested refinement targets are provided in the "Additional information" field for the targets. Coordinates of the starting models are available from the field "Template". Please, submit your refined models the same way you do for the regular predictions, remembering that names for the refinement targets start with "TR" instead of "T0".

Next week we are planning on adding several more targets to the refinement experiment and 10 targets for regular predictions.

CASP organizers
T0581 category change and Refinement targets(2010-6-23)
We originally released target T0581 as a server only target. After more careful consideration it appeared that this target is one of the more challenging targets to predict. We would like to suggest this target for prediction to human groups and shift it to human/server prediction category. To allow extra time for expert prediction, we are extending human deadline for T0581 by July 11.

We also will be releasing our first refinement targets this week. Please check our Refinement Target List link from the main CASP9 web page.
CASP9 update - May 14(2010-5-14)
In our previous communication we stressed that human-expert structure predictors are recommended to concentrate their efforts on modeling of Human/Server targets. We want to emphasize here that all groups (including human-expert) that plan to predict in DR/RR/FN/QA categories are expected to submit their predictions on all targets, i.e. both - "Human/Server" and "Server only".

Disorder region predictors have been informed by the organizers that we had started enforcing the rule
that the residues predicted to be in the disordered state should have probability scores >0.5, while those in ordered state - less than 0.5. For those who are still planning to submit DR predictions - please make sure that your format comply with the requirements posted at our website.

Next Monday we will release one big target (887 residues) that will be followed by 10 to 12 other targets throughout the week.

CASP9 organizers
CASP update - May 7(2010-5-7)
First week of CASP9 prediction season is over. We have released 14 targets. The vast majority of them were easy TBM targets. Next week you will find some harder targets in the human prediction category.

As of today, we have 125 groups (predominantly servers at this early stage) contributing models to the Prediction Center. You can always find the latest CASP statistics at http://predictioncenter.org/casp9/numbers.cgi .

In CASP9, we are planning on releasing between 50 and 60 targets for human-and-server prediction and approximately twice as much targets (depending on their availability) for server-only prediction. Assessors will be comparing all participating predictor groups on the subset of Human/Server targets and, additionally, the server groups on all released targets. The human-expert groups should concentrate on predicting structures for the Human/Server targets. Those, wishing to take the challenge and predict all of the released targets (including the "server-only" ones) are welcome to do so but the evaluation emphasis will be placed on the "Human/Server" targets. Subject to availability, we will give priority to releasing targets containing low homology domains in the Human/Server track.

Reminding that we are accepting multimeric predictions this CASP. So far, we received such predictions from 9 servers.

Tarballs of tertiary structure models from servers are made publicly available at http://predictioncenter.org/download_area/CASP9/server_predictions/ the next day after a particular target is closed for server prediction, i.e. on the forth day after the target release, at 7:45am PDT. Approximately an hour later these tarballs are submitted to the quality assessment (QA) servers, which have an extra 3 days to submit their QA predictions. Deadline for human-expert QA predictions is the same as for all other types of prediction.

On the weekend days we will be submitting subsequent targets to the QA servers.

Next Monday we will release 2 new targets for prediction in all prediction categories.

Have a productive next week of CASP!

CASP organizers
May 3 - CASP9 starts(2010-4-29)
We are happy to inform you that as of today, April 29, we already have 100 human-expert groups and 125 automatic servers registered for the CASP9 experiment. With practically all CASP8 "winners" already on board and around 20 "new kids on the block", we are anticipating another exiting prediction season. Structural Genomics centers have started submitting sequences for potential targets to us and we have already prepared enough targets to run the first 2 weeks of the experiment at full load.

We will kick off the 9th round of CASP experiments with two relatively easy targets next Monday, May 2. These two targets will be followed by three targets Tuesday through Friday totaling 14 targets for the first week. To start it gently, we will not be releasing very hard for prediction targets this week. The first difficult targets are expected to be released starting the second week of the prediction season.

Reminding you that according to the decision of the CASP8 predictors' meeting we are reviving quaternary structure prediction in CASP9. We will advise you on the possible oligomeric state of the particular target protein if such information is furnished to us by the experimentalists. We want to stress out that this information should be taken just as an advice on the MOST PROBABLE quaternary state of the target as data on many of the CASP targets are coming to us when structure refinement is still in progress and therefore experimentalists can not be sure of the final assignments. Format for the multi-chain predictions is described at the CASP9 format page:
http://predictioncenter.org/casp9/index.cgi?page=format#TS , and shown in the Example 4 there.

Andriy Kryshtafovych
for CASP9 organizers
Second round of the dry run for servers(2010-4-20)
We have finished the first round of checking connectivity and format compatibility with the registered servers.

All non-QA servers were sent a query and we expected that all of them should have returned predictions by now (more than 3 days after the request). If your server did not get a query or did not send out a prediction - it's time to check for the problems and get in touch with the organizers. During the last 4 days we were able to identify and fix problems for the majority of 100+ servers registered for CASP9. Those server curators who haven't managed to make their servers work properly yet - don't hesitate to contact me in case you need help from the organizers' side.

Today we start a second round of the dry run for all registered CASP9 servers. In a few minutes we will be sending another test "target" to all non-QA servers. In the evening (Pacific Time) we will be sending a tarball from the first test "target" T0987 to the Quality Assesment servers.

Based on the first round of the dry run we can see that almost all of HTTP servers reply either with the web page or an email about their target receiving. This is not the case, though, for almost half of the email servers. So, email server curators: please, make sure that your servers reply to our distribution server casp8-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0987 - query received by MY_SERVER". This will help us to track whether your server received a request from us so that we can timely address any connectivity issues. The prediction itself should be sent to the address specified in the REPLY-E-MAIL field of the query (please note that this address should be always taken from our query and not hard-coded as we may change it during the season).

Reminding you that during the dry run, you will be receiving both, acceptance and rejection messages from our verification server. During the regular CASP season it will be possible to check status of your server submissions through the link Server Predictions from the CASP9 web page: http://predictioncenter.org/casp9/status_n.cgi (link itself is already operational though not posted to the CASP9 web page yet).

Also, you can see all of your accepted predictions through the "My CASP9 profile" link from the CASP9 submenu on the left side of the CASP9 web page. The direct Model Viewer link will be available during the regular season from the CASP9 web page: http://predictioncenter.org/casp9/groups.cgi .
Server dry run has started(2010-4-16)
At this, first stage of the dry run we are testing servers returning predictions in all formats but QA. Quality assessment servers will be tested starting next Tuesday.

During these tests you will be receiving both, acceptance and rejection messages from our verification server. During the regular season, though, acceptance messages will be turned off.

A request to all EMAIL-server curators: please, make sure that your servers reply to our distribution server casp8-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0987 - query received by MY_SERVER". This will help us to track whether your server received a request from us so that we can timely address any connectivity issues. The prediction itself should be sent to the address specified in the field REPLY-E-MAIL of the query (please note that this address should be always taken from our query and not hard-coded as we may change it during the season).
Server dry run reminder(2010-4-14)
We were notified by several server curators that their servers are still in the process of preparation for CASP9 dry run. To allow them some extra time, we are postponing testing connectivity with the servers for two days. Also, we advise those caspers who plan to participate in server track but have not registered their servers yet to do it immediately. On Friday, April 16, 2010 we will send a test target (T0987) to the registered servers. Please respond as you would for CASP9 targets. Of course, these predictions will not be part of the CASP9 experiment.

We will be sending 3 variables to your server's submission URL (or email): the SEQUENCE, the TARGET-NAME and the REPLY-E-MAIL (where to return the results). For the quality assessment servers we will be sending the TARBALL-LOCATION variable instead of (or in addition to, if you specify so) the SEQUENCE. Please, make sure you provide the required parameters in your CASP8 server registration.

IMPORTANT THINGS TO REMEMBER

There will be no essential changes in the procedures for submitting targets and accepting predictions comparatively to the CASP8. For CASP novices, helpful information can be found below in this announcement and at http://predictioncenter.org/casp9/registration.cgi , http://predictioncenter.org/casp9/index.cgi?page=format .

1. Target distribution procedure for servers.
You will be receiving CASP9 queries from the distribution server in Davis casp8-meta@predictioncenter.org and the results will be collected directly by the Prediction Center. At the end of each week we will try to notify you about how many targets we plan to release the following week. Targets are planned to be released on business days only. We plan not to exceed a load of 3 targets per day for servers. Targets will be made available and requests to all servers will be sent around 9am PST. The submission engine will resend the query if it encounters obvious connecting problems (network timeouts, 'no response' etc.). Failures that go beyond that require special attention, but we'll make every effort to notify server curators ASAP if we suspect something is not working. The facility that allows checking data flow status by server predictors will also be available.

2. Server submission format.
Please submit your predictions in the standard CASP format. Your submissions will be immediately verified at time of submission. CASP warning and error messages will return directly and immediately to you, and will refer to the material you submitted, allowing you to respond in close to a server time frame, if necessary. Please note that, as in previous experiments, no prediction will be finally accepted by CASP until it passes CASP format verification. Please, consult the CASP format description page for details:
http://predictioncenter.org/casp9/index.cgi?page=format

3. The timeframe for server prediction acceptance is the following. All server groups have 72 hours since target distribution to return the prediction. Notifications will be sent to the server contact person's email address only in case of errors encountered. If your prediction doesn't pass the CASP verification system, you will need to correct your format and manually resubmit the corrected prediction to the email servers@predictioncenter.org within the original 72-hour window. After 72 hours no server predictions will be accepted or altered in any way. If you expect your server to work on prediction generation more than 72 hours, then we would advise you to register a regular (not server) prediction group for CASP9 instead.

In addition to notification emails, you will be able to check the submission status of your prediction through the Server Submission Status Page or through the Model Viewer facility.

CASP9 organizers
CASP9 - registration(2010-3-29)
The registration for CASP9 experiment is now open.

To register for the experiment, you will need to register with the Prediction Center (PC) first (if you haven't done this yet). At this step we will collect the basic registration information to be used for your participation in CASP9, all subsequent CASP experiments, between-CASP initiatives, and local services. The information provided by you will not be shared with anyone outside of the CASP system.

After you register with PC and login to our website, go to the CASP9 web page, where you will be able to register for the CASP9 experiment (a separate registration form under the CASP9 menu). You will find five separate registration forms there. Please, read the registration instructions and use the appropriate form.

We ask that you register with the Prediction Center at your earliest opportunity as we plan to release future CASP9-related news mainly through our website. We recommend that you select an option "Subscribe for Prediction Center newsletters" as in this case you will be receiving emails every time the news are posted on our website. This functionality was just recently added to our registration form. So, if you have registered earlier, please go to "My personal Data" link and select this option.

Also, we ask server group leaders to register as soon as possible as we are planning on testing the connectivity with the registered CASP9 servers starting April 14, 2010. The details of the dry run will be posted in the Message Board section of our website shortly (this section is available from both the Prediction Center home page and the CASP9 home page).
Blue Waters computer(2009-12-14)
Dear CASP Participant:

You might like to know that NSF is soliciting proposals for developing applications for the Blue Waters computer, due to come on line in the next year. As you know, there is a lot more interest in compute intensive methods of modeling protein structure than there was a few years, and this is an opportunity for those of you who can see possibilities in another couple of orders of magnitude of compute power to get unique resources. NIGMS is involved in this because they are interesting in encouraging projects in the area of protein folding and structure modeling, among others.

There is a webcast this Thursday, at which you can get more specifics. The NIH announcement (From Peter Preusch is as follows:

"NIGMS seeks your input on areas of science that would benefit from access to the latest generation high-performance computer. The Blue Waters petascale computing system, which is under construction by the National Center for Supercomputing Applications (NCSA) at the University of Illinois and funded by the National Science Foundation, will be the most powerful computer in the world when it comes on line in 2011. Details of the capabilities and architecture of the Blue Waters computing system are available at http://ncsa.uiuc.edu/BlueWaters.

This message is to alert you to the opportunity to apply for allocations of computing time on the Blue Waters computing system and to help organize collaborative groups to submit high-impact community applications for time on this new machine.

NIGMS is facilitating the formation of collaborative groups by:

1) Hosting a virtual workshop and applicant briefing videocast, NIGMS-NSF Briefing on Blue Waters High-Performance Computing Opportunities, Thursday, December 17, 2009 at 2:00 - 4:00 p.m. on the opportunity to apply to NSF for allocations of computing time on this important new resource.

2) Providing a Web site where you can share ideas on areas of science that could benefit from access to this resource and express your interest in joining or leading a group of scientists in an application to the NSF.

For additional information, visit http://www.nigms.nih.gov/bluewaters."


John Moult.
CASP9 meeting venue and dates(2009-11-16)
CASP9 predictors' meeting will take place at the Asilomar Conference Center, Pacific Grove, California on December 5-9, 2010. Details of the future CASP9 experiment are available from the Prediction Center website.
CASP9 preliminary timetable(2009-9-11)
CASP9 experiment will be run May through July 2010.

Tentative dates are as follows:
March 30, 2010 - registration starts
April 14 - server "dry run" starts
May 3 - first targets will be released on or shortly after this date;
July 17 - last targets will be released not later than this date;
July 31 - prediction season ends;
December 2010 - the predictors meeting takes place at the Asilomar Conference Center in Pacific Grove, CA, USA.

CASP9 organizers
CASP8 domain definition and coordinates(2008-11-21)
We have released the official domain definitions and coordinates used for CASP8 evaluations. CASP8 Abstract book is also available from our website. Results of the automatic evaluation of the predictions will be available one week before the meeting.

CASP8 organizers
Arriving to Sardinia(2008-11-16)
A few important information about your travel to Sardinia:

Once you get to the airport of Cagliari, there are two ways to get to the hotel:

By bus: You take the ARST bus to Cagliari. the timetable can be found at http://www.sogaer.it/aeroporto/pullman/ . The cost is 2 Euro and the ticket can be bought at the automatic machines located in the hall of the airport.
The bus leaves you at the bus station in Cagliari. The station is on a square (Piazza Matteotti). You take the bus PF (direction Fiumini) and get out at the Hotel Setar stop (about 40 minutes). The ticket is 1 Euro.

You can take a taxi. The cost is about 40-50 Euro. Please only take official taxis and ask the driver the approximate cost to Hotel Setar.
There will probably be several people coming to CASP in your plane. You might want to share a taxi with them.

Meals included with your hotel room: from dinner on the day of arrival to lunch on day of departure. Any other arrangement should be made directly with the hotel. The cost of an extra lunch or dinner is 22 Euro.

The hotel bill should be settled upon arrival.

The hotel has wireless in all common areas and in most of the rooms.
CASP8 junior scientist session(2008-10-28)

Dear CASP Participants,

During the CASP8 meeting we will dedicate a special session to topics
suggested by junior scholars. We will also award a poster prize and invite
oral presentations. All students, postdoctoral associates, and others young
at heart are welcome to participate (only junior scholars will be eligible
for awards ;-)).

Our goal is to select areas that are of particular interest to the
community of young scientists. Please send suggestions /issues to be
discussed to Krzysztof Fidelis (kfidelis@ucdavis.edu). We would also
welcome volunteers wishing to help organize this session (contact Krzysztof).

Krzysztof Fidelis
CASP8 job fair(2008-10-28)
Dear CASPers,

we would like to take advantage of the CASP8 meeting to help young scientists looking for a position in Computational Biology meeting potential group leaders and vice versa.

We plan to organize an afternoon to get them together for interviews / informal meetings /etc.

If you are looking for a position, could you please send your cv to anna.tramontano@uniroma1.it by the 9th of November?

If you have positions available could you please send a mail with the advert to anna.tramontano@uniroma1.it by the 9th of November?

As soon as we have an idea of how many people are interested in this initiative, we will get back to you with more information.

Thank you very much

The CASP organizers
CASP8 fellowships(2008-10-15)
We have now completed awarding CASP8 registration fee /lodging /travel fellowships and the recipients have been notified. The CASP8 speaker selection will be completed around Oct. 23. CASP8 speakers will be offered registration fee waivers, as well as lodging and travel reimbursements. At the same time we are extending early registration rate deadline to Oct. 27.

CASP8 organizers
CASP8 meeting registration; December 3 - 7, 2008; Sardinia, Italy(2008-9-18)
Registration for the CASP8 meeting is now open. We expect that this year we will be able to accommodate all the people wishing to participate. The Meeting Registration Form is available at:
http://predictioncenter.org/casp8/meeting_registration.cgi .

Meeting fees consist of a registration fee and a lodging fee for four nights (December 3-7). Rough estimate of total meeting fees (full board) for an academic participant is $880-$1050 depending on the accommodation choice. Details are provided in the registration form.

A limited number of accommodation fellowships and travel fellowships will be available. However, registration should not be made contingent on an accommodation or travel award.

Predictors attending the meeting are also required to ensure that a long abstract and a questionnaire (if requested by assessors) describing their group's method have also been submitted. A web page for submitting your abstract is available at http://predictioncenter.org/casp8/abstracts.cgi .
Please note that meeting registration will not be complete without submitting these materials.
Last 5 targets for refinement(2008-8-2)
Five targets for the refinement experiment have been released yesterday and today. The details of the suggested refinement targets are provided in the pdb files for the starting models and in the "Additional information" field for the targets. All in all, we released 12 targets (14 domains) for the refinement experiment in CASP8 .
End of CASP8 target release(2008-7-18)
With the two server-only targets today, all CASP8 targets have been made available for prediction. In this round of CASP we have released 128 targets including 57 human/server targets. One target has been canceled so far. We expect the corresponding structures to be gradually released by the PDB. We regularly update our target list to indicate which targets have already appeared in the PDB. Please, check our target list for updates on Wednesdays. At this time we have structures for 34 CASP8 targets available.

Please note, that we will still be releasing targets for the refinement experiment. You may expect new refinement targets within the next two weeks. This week we have released 3 more targets for refinement.

CASP organizers
Human/server targets are over(2008-7-12)
We have finished releasing human/server targets for prediction in CASP8. Last week we released more targets of this type than usual in order to give you full 3 weeks to predict each of them. All in all, we released 57 human/server targets in 11 weeks of the experiment or roughly 1 target per business day. Next week is the last week of CASP8 target release and we will be releasing "server only" targets.
T0472 - canceled for human predictions(2008-7-9)
Target T0472 has been canceled for human predictions as the corresponding structure had been released by the PDB. The target is turned over to the "server only" status and will not be assessed in the human-track part of CASP8.
Refinement targets - 3 proteins (4 domains)(2008-7-8)
Please, pay attention that 3 targets for the refinement experiment have been released today. The details of the suggested refinement targets are provided in the pdb files for the starting models and in the "Additional information" field for the targets.
T0465 - switching to human/server target(2008-6-30)
We are switching T0465 over to human/server target. In order to provide enough time for human-regime modeling, we are adding 10 extra days to the prediction window for this target so that it will expire for human prediction on July 21.
No targets on July 4 (2008-6-27)
Next week we will have no targets released on Friday. Next target release date after the holiday - July 7.
Extended timeframe groups(2008-6-24)
We are launching an additional service designed to help test methods requiring more time than the usual 3 weeks allowable in CASP8. Registering an additional “extended timeframe” group will provide a time stamp certifying the PRE-diction nature of the submitted models as well as CASP numerical evaluation results in the familiar format. Please note that the predictions sent by an "extended timeframe" group WILL NOT be part of the CASP8 experiment, WILL NOT be included in the final results tables and WILL NOT be assessed by the CASP assessors.

Please, use the appropriate registration form ONLY if you feel that you will need more time than the usual 3 weeks for submitting predictions. Predictions from the "extended timeframe" groups will be accepted for 6 weeks total. If the experimental structure becomes publicly available during the extended time window, the predictions accepted after that date will be discarded. Prediction Center does not fully control the extended deadlines and there is real risk that already submitted predictions will be discarded.
CASP8 update. New fold targets appeal. Refinement targets.(2008-6-10)
General participation statistics
We are in the middle of the CASP8 prediction season. Interest in the CASP experiments remains high. We have 221 groups including 121 servers actively participating in CASP8. More than 28 thousand predictions have been collected by the Prediction Center in the first 5 weeks of the experiment.

Targets
Fifty nine targets (including 28 human/server targets) have been released during the first part of the CASP8 experiment. As you may have noticed, there have so far been few small ‘new fold’ or very remote fold proteins suitable for testing non-template based modeling methods. This is starting to look like a problem, since, obviously, it's very important the community does find out how those methods are progressing.

So we are writing with an urgent appeal to help find target or targets of this type (typically 150 residues or less). Larger proteins with suitable semi-autonomous domains would also fill this need. For those, we need the relevant domain boundary information to be provided with the target. Please go and pester your friendly experimental colleagues, and see what you can come up with.

Refinement targets
The first target has been released for model refinement (TR389). The experimentalists kindly provided us with the coordinates for this target ahead of time. After the automatic evaluation of the models we want to suggest you one of the best models for refinement. Please, pay attention that the refinement target names start with "TR" instead of "T0" for regular targets.

CASP organizers
FORCASP migration(2008-5-19)
We are moving FORCASP discussion forum from the forcasp.org website to the predictioncenter.org site (link FORCASP forum is added to the menu). Old posts remain available at the forcasp.org website.
CASP organizers
Prediction in non-tertiary structure categories(2008-5-16)
Some targets in CASP8 Target List are marked as 'Human/server' and the others as 'Server only'. We have informed you that the human-expert groups should concentrate on predicting 3D structures for the Human/Server targets as the assessors will be comparing human-expert groups on this subset of targets. We want to clarify that this requirement pertains to the tertiary structure predictions only. Human-expert groups are expected to submit predictions for all targets (both "Human/Server" and "Server only") for the categories other than TS.

CASP8 organizers
Request for CASP8 targets(2008-5-7)
Dear CASP8 participants,

The CASP8 prediction experiment has just begun, and as always, it will only work if we have the help of the experimental community in providing targets.

Many targets have been provided by structural genomics centers in the last two CASPs, and expect to that will be the case again this time. However, we still very much need targets from the broader structural community. We need all sorts of targets but in particular, there are several sorts of targets we expect to be short of.

1. We expect the number of ‘new fold’ provided by the SG centers will be smaller this time, and we really really need these to test ‘ab iniito’ target prediction methods. So if you have one, we would be very very grateful if we could use it as target.

2. We want to improve our test set for assessing disorder prediction methods, so if you have structure that contains significant disorder, we would very much appreciate using it as a target.

3. In all the CASPs to date we have only ever had one membrane structure target, so if you have you could make available, that would be great.

CASP only succeeds because of the support and co-operation of the members of this community, and we very much need your help.

The time table is similar to other CASPs: The prediction season opened at the beginning of May, and will run until the end of July. We will release targets continuously throughout that period, as evenly spaced as possible, and hope to have about 100 targets altogether. Each target will be available for prediction for a period of three weeks, although in some cases we request a longer period to allow it to be used to test refinement methods. It is of course important that there not be any kind of public release of the experimental structure (including things like pictures on web pages or abstracts) until after the predictions for that target are closed.

It’s fairly simple, with just two things to bear in mind. First, because of the timing framework, there needs to be at least a month between the submission date and any release of the structure. Second, we ideally need the experimental co-ordinates by the beginning of August and definitely by the beginning of August, so that the predictions can be assessed. At that point, they can be kept confidential if necessary, though we would like to provide them to predictors of your structure at the beginning of November at the latest, so that can see how well they have done. Participants would also usually like to be able to show slides and discuss their predictions at the meeting at the beginning of December.

So, if you have any thing suitable, we would be most grateful if you would enter the data on the web form: http://www.predictioncenter.org/casp8/targets_submission.cgi
OK, that's about it. Please get in touch if you have any questions or concerns. Hoping for lots of targets....

CASP8 organizers
CASP8 started(2008-5-5)
We have released the first two CASP8 targets. Good luck everyone in predicting these and all the subsequent CASP8 targets.

Please, pay special attention to the column "Type" in the Target List. In the current CASP experiment we are planning on releasing between 50 and 60 targets to be evaluated in the human and server track and many more targets (depending on target availability) to be evaluated in the server-only track. Assessors will be comparing all participating predictor groups on the subset of Human/Server targets and, additionally, the server groups on all released targets. The human-expert groups should concentrate on predicting structures for the Human/Server targets. Those, wishing to take the challenge and predict all of the released targets (including the "server-only" ones) are welcome to do so but the evaluation emphasis will be placed on the "Human/Server" targets. Subject to availability, we will give priority to releasing targets containing low homology domains in the Human/Server track.

Server predictions for all targets will be made publicly available immediately after acceptance by the CASP verification system. Receiving status of server predictions can be checked from the main CASP8 web page by following the link "Server Predictions." Please note that tarballs of all 3D models (with AL predictions already converted into coordinates) will be posted at the same place usually with one-day later. The electronic address of these tarballs will be sent to the quality assessment (QA) servers 4 days after the original target release. QA servers will have an extra 3 days to submit QA predictions.
CASP8 server dry run - April 28(2008-4-28)
On April 28 we will have the last round of dry runs for the servers. Please get your servers ready.
The first CASP8 targets will be released on May 5.
CASP8 server rules(2008-4-2)
CHANGES relative to CASP7

There will be just minor changes to the rules for server participation in CASP.

According to the suggestions of CASP7 predictor meeting, in CASP8 we are extending the window for accepting server predictions. Servers will now have full three days to return the prediction. No additional time for corrections will be allotted but corrections will be accepted within the original 72 hour window.

Also, according to another recommendation of the CASP7 predictor meeting, we will have two different sets of targets for evaluation in the human-and-server track and in the server-only track. We plan to release as many targets as possible for evaluation in the server-only track and a subset of around 50 targets from among these for the human-and-server track.

For the servers participating in the model quality assessment category, we will be sending a link to the tarball of accepted server structure predictions on a particular target in 1 business day after closing the window for server 3D predictions. The quality assessment servers will have another 3 days to generate the model quality assessment prediction.

DRY RUN

We will be testing connectivity with registered CASP8 servers starting on April 14, 2008. To test your server, we will send you an old CASP7 target (T0283). Please respond as you would for CASP8 targets. Of course, these predictions will not be part of the CASP8 experiment.

If your server participated in CASP7, we expect the test to be just a formal recheck. For new servers: we will be sending 3 variables to your server's submission URL: the SEQUENCE, the TARGET-NAME and the REPLY-E-MAIL (where to return the results). For the quality assessment servers we will be sending the TARBALL-LOCATION variable instead of (or in addition to, if you specify so) the SEQUENCE. Please, make sure you provide the required parameters in your CASP8 server registration.

IMPORTANT THINGS TO REMEMBER

1. Target distribution procedure for servers.
You will be receiving CASP8 queries from the distribution server in Davis and the results will be collected directly by the Prediction Center. At the end of each week we will notify you about how many targets we plan to release the following week. Targets are planned to be released on business days only. We plan not to exceed a load of 3 targets per day for servers. Targets will be made available and requests to all servers will be sent around 9am PST. The submission engine will resend the query if it encounters obvious connecting problems (network timeouts, 'no response' etc.). Failures that go beyond that require special attention, but we'll make every effort to notify server curators ASAP if we suspect something is not working. The facility that allows checking data flow status by server predictors will also be available.

2. Server submission format.
Please submit your predictions in the standard CASP format. Your submissions will be immediately verified at time of submission. CASP warning and error messages will return directly and immediately to you, and will refer to the material you submitted, allowing you to respond in close to a server time frame, if necessary. Please note that, as in previous experiments, no prediction will be finally accepted by CASP until it passes CASP format verification.

Below we summarize differences in format of server submissions from that of human groups.

2.1 Header AUTHOR should contain your group name instead of the 12-digit predictor code, e.g.
AUTHOR 3D-JIGSAW
or
REMARK AUTHOR 3D-JIGSAW

2.2. Header SCORE in your prediction is allowable and optional (a real number reflecting self-estimation of the prediction quality).

2.3. For servers, it is allowed to have several models for the same target in one file. If your server returns only one file with several models, we will preprocess such an entry. You may add only one set of required header fields (PFRMAT, TARGET and AUTHOR) at the beginning of the file. Our script will split a multiple model file into separate files (one model per file) and only then we will send each model separately to our verification software (models numbered 6 and higher will be ignored). Error messages (if any) will be sent for each model separately. So you will be able to correct models (if needed) separately.

3. The timeframe for server prediction acceptance is the following. All server groups have 72 hours since target distribution to return the prediction. Error notifications will be sent to the server contact person's email address. If your prediction doesn't pass the CASP verification system, you will need to correct your format manually and resubmit the rejected prediction within the original 72-hour window. To do this, you will need to include the following line in your revised prediction:
REMARK Corrected server submission
and send it by email to: servers@predictioncenter.org .
After 72 hours no server predictions will be accepted or altered in any way. If you expect your server to work on prediction generation more than 72 hours, then we would advise you to register a regular (not server) prediction group for CASP8 instead.

You will be able to check the submission status of your prediction through the Server Submission Status Page or through the Model Viewer facility.
CASP8 registration (2008-3-22)
The registration for CASP8 experiment is now open.

To register for the experiment, you will need to register with the Prediction Center (PC) first (if you haven't done this yet). At this step we will collect the basic registration information to be used for your participation in CASP8, all subsequent CASP experiments, between-CASP initiatives, and local services. The information provided by you will not be shared with anyone outside of the CASP system.

After you register with PC and login to our website, you will be able to register for the CASP8 experiment (a separate registration form under the CASP8 menu). You will find five separate registration forms there. Please, read the registration instructions and use the appropriate form.

We ask that you register with the Prediction Center at your earliest opportunity as we plan to release future CASP8-related news mainly through our website. We recommend that you select an option "Subscribe for Prediction Center newsletters" as in this case you will be receiving emails every time the news are posted on our website. This functionality was just recently added to our registration form. So, if you have registered earlier, please go to "My personal Data" link and select this option.

Also, we ask server group leaders to register as soon as possible as we are planning on testing the connectivity with the registered CASP8 servers starting April 14, 2008. Server participation rules and the details of the dry run will be posted in the Message Board section of our website shortly (this section is available from both the Prediction Center home page and the CASP8 home page).
CASP 7.5 meeting(2008-2-1)
Together with CNIO, Madrid, we are organizing the next between-CASP meeting (CASP7.5). It is going to take place in Madrid, Spain in April 2008. The idea of the between CASP meetings is to update the progress of structure prediction as measured by the CASP experiments. In contrast to the full CASP meetings that are exclusively for participants and developers, this meeting will be open to all interested scientists. All interested please check the meeting web page: http://ubio.bioinfo.cnio.es/casp/index.html
CASP8 preliminary timetable(2008-2-1)
Registration for the experiment will start in the last week of March 2008.

Prediction season will run from early May through early August 2008. The first prediction targets will be released not earlier than May 5, 2008; the last prediction targets will be released not later than July 18, 2008; prediction season will end not later than August 1, 2008.
According to the recommendations of the CASP7 predictors meeting, we will be releasing about 50 targets for evaluation in the human and server track and as many targets as we can for evaluation in the server-only track (including "human and server" targets). The human-expert groups wishing to take the challenge and predict all of the released targets (including the "server-only" ones) are welcome to do so but the evaluation accent will be placed on the selected targets. Subject to the availability, we will give priority to targets containing low homology domains for inclusion in the human-expert modeling experiment.
The meeting to discuss results of the experiment will be held on the island of Sardinia, Italy, December 3-7, 2008. The meeting will take place at Hotel Setar , near Cagliari. The hotel is located in Quartu S. Elena, 10 kilometers from Cagliari and 15 from the Cagliari airport.
CASP10 dry run for servers(2008-1-1)
Dear Caspers,

As of today, 72 prediction servers have been registered for CASP10 experiment. We have started checking connectivity and correctness of prediction format for the servers in non-QA prediction categories. We have sent them 1-3 requests to predict the test target T0921. If you had registered a TS, RR, DR or FN server, but have not received at least one request from us - please check your registration settings and contact us if in doubt. Quality assessment servers will be tested starting tomorrow afternoon (PST). We also plan to send one more modeling request to all registered non-QA servers tomorrow morning (PST). So, if you plan to participate in the server track but have not registered your server(s) yet - we advise you to do so immediately. During the tomorrow tests you will be receiving both, acceptance and rejection messages from our verification server. During the regular season, though, acceptance messages will be suppressed.

A request to all EMAIL-server curators: please, make sure that your servers reply to our distribution server casp-meta@predictioncenter.org immediately after you have received a query. Please put the following text into the Subject of the email: "T0921 - query received by MY_SERVER". This will help us to track whether your server received a request from us so that we can timely address any connectivity issues. The prediction itself should be sent to the address specified in the field REPLY-E-MAIL of the query (please note that this address should be always taken from our query and not hard-coded as we may change it during the season).

CASP organizers
Protein Structure Prediction Center
Sponsored by the US National Institute of General Medical Sciences (NIH/NIGMS)
Please address any questions or queries to:
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