Seventh Community Wide Experiment on the Critical
Assessment of Techniques for Protein Structure Prediction
The same form allows registering for the Student Addendum Conference (SAC-CASP7). You will receive a separate letter from the organizers of SAC-CASP shortly.
As previous meetings, CASP7 has limited attendance. To expedite the registration
acceptance and to allow earlier completion of the travel arrangements we will follow
the rules outlined below:
1. Early registration is strongly encouraged and preference will be given to those registering early.
2. Each research group having submitted predictions to CASP7 will automatically be guaranteed one registration. For the purpose of meeting registration, a research group is equivalent to an academic unit, i.e. CASP prediction groups with the same group leader will be considered as a single academic unit. The first person in the group does not need to wait for our confirmation and may proceed with travel arrangements immediately. However, we reserve the right to deny the registration if more than 1 person from the same academic unit registers as Group representative #1 or #2 (form).
3. Second registration per group will most likely be available. We will send confirmations by September 15.
4. People who have not predicted and additional group members will receive notification by the end of September.
Meeting fees include registration fee and lodging/meals fee. No payments should be sent at this time. Payment will be expected promptly following a separate email confirmation from the organizers. Details on how to submit payment will be provided shortly. There will be absolutely no refunds.
A limited number of Asilomar accommodation fellowships and travel fellowships will be available (refunds for American carriers only). However, registration requests should not be made contingent on accommodation or travel award. People who register should be prepared to cover the Registration Fee and the Asilomar Lodging /Meals Fees.
We will very much appreciate your feedback on the organization and running of the CASP7 experiment this year. Please fill out the form at
http://www2.predictioncenter.org/casp/casp7/public/cgi-bin/polling.cgi
At the moment the only two targets that are left unexposed for the refinement are TR368 and TR370. Concerning TR370, we want to emphasize that the corresponding experimental structure (T0370) appears to be a tetramer and there are several places where inter-subunit interactions most likely influence conformation of loops. It is obviously a very hard case for the refinement but we want to give it a try and estimate how much missing these interactions influenced the refinement results. You can also see that the similar situation takes place for TR380.
Reminding that CASP7 meeting registration will start in September. You may also start thinking about the abstracts, which we will be collecting next month.
It probably makes no sense to remind you that the prediction season ends next Monday. Many of you have been waiting for that day to finally get that deserved rest! But we do want to remind you that there is a possibility that the refinement experiment will be going on for 3 more weeks as it was originally scheduled. Just a few hours ago we received several structures for CASP7 targets, some of which can be suitable for the refinement. Please check our refinement page on weekend and on Monday to see whether new targets were released for the refinement. For various reasons, it was hard to pick targets for the refinement experiment. As you can see, we had only three so far. And it is very sad that we had to cancel one of them (TR366) because of the early release.
This is the last of our regular Friday update messages for the season. From now on we will be keeping you informed about the CASP post-season developments through occasional emails and postings at this web page. Thank you all for participation and good luck!
The facility for accepting server predictions has been shut down. Tomorrow we are also closing the facility for accepting server corrections.
One more target for refinement was added today - please, check our Refinement page. We are considering a few more targets for the refinement experiment.
It was brought to our attention that some people have misread instructions posted at our submission page. Specifically, updating an original prediction has been attempted by pasting into text box (1) of the Prediction Submission Form AND specifying the PIN number of the original prediction in field (3). We want to clarify that the PIN-number option should only be used for making corrections to the original model directly on the web page. We have also added a functionality to disallow simultaneous use of any two submission options.
All in all, we have received 154 submissions of which we selected 104 targets for CASP7, and as of today 98 of these have been released. This means that we are left with 6 targets for next week. We plan to release three targets on Monday, two on Tuesday and the last one on Wednesday. To reduce possible overload in the last week, we are extending the prediction season by 3 days. The deadline for the last CASP7 target will be August 7.
At the end of the target release season we would like to thank all the crystallographers and NMR spectroscopists who supported the experiment. Especially big thanks go to the four structural genomic centers (JCSG, MCSG, NESG and SGC) which provided the biggest share by submitting 20+ targets each. The full list of the people/centers submitting targets for CASP7 will be published shortly at the CASP7 target submission page.
We also want to thank the PDB for arranging a special mechanism so that the proteins deposited to the PDB with the "CASP" annotation were put on hold for at least 4 weeks.
This week we had to cancel target T0377 as its structure had been released by the PDB (2ivy). Second time this season a different crystallography center independently solved and published the structure submitted to CASP.
Complete list of targets (13) for oligomeric predictions:
T0295, T0300, T0305, T0308, T0310, T0332 (expired);
T0338, T0339, T0343, T0346, T0366, T0372, T0375 (valid for prediction).
Complete list of side chain refinement targets (6):
T0326, T0340, T0345, T0346, T0359, T0366
Targets for high accuracy assessment:
Not specified in advance, this will be determined by the assessors.
Targets for refinement:
TR288, TR308; additional targets are considered.
Warning for server groups.
We want to remind that the extra 24 hour grace period in addition
to the regular 48 hours for accepting server predictions is intended
solely to allow correcting any technical errors and not for changing
the prediction content. Our policy is to reject the prediction if
there exists an evidence that someone attempted to manipulate the
deadlines. We may make server corrections public in the future.
Side chain refinement targets.
T0326, T0340, T0345, T0346 (already announced); T0359 (released this
week), T0366 (to be released next Monday).
Multimers.
Three new multimers were released last week:
T0338, T0339 and T0343.
They are available for prediction in the oligomer format
(additionally to the usual CASP monomer prediction).
List of other targets for oligomer predictions:
T0295, T0300, T0305, T0308 (expired);
T0310 (to expire next Monday);
T0332 (to expire on Jul 8).
Side chain refinement targets.
T0326 (already announced);
T0340 (released this week);
T0345 and T0346 (to be released next Monday).
Model Refinement.
We are clarifying details of 3 more potential targets for
model refinement with the crystallographers. Next week we
will issue an announcement if any of these targets proved to
be suitabile for refinement.
T0308 has been released for refinement (June 27).
Multimers.
Besides T0295 and T0300 (already closed), we are accepting multi-chain
predictions for T0305, T0308, T0310 and T0332. Please check June 9 post
below for format.
4 targets have been released by the PDB.
Besides T0295, three other CASP structures have been released by the PDB
this week T0290, T0291 and T0293 (see our target list page). So, you may
check now how well you did on these targets.
T0288 - refinement.
We have finished preliminary automatic evaluation of 3D predictions
submitted on T0288. Analysing results, we were "disappointed" to learn
that initial modeling went very well leaving not much room for the
refinement. Nevertheless, we want to proceed with our initial intention
and do suggest one of the best models for this target for refinement.
This task is pretty challenging but we can see that there are some
details in the prediction that can be improved. The model selected for
the refinement can be found following "Refinement" link from Targets
section of the casp7 web page. Your refined models should be submitted
as regular TS predictions for the target TR288.
We asked our colleague experimentalists to extend public release date for a couple of targets that we wanted to suggest for model refinement (we are planning on having a few more of these by the end of the prediction season). First of these targets, T0288, has expired for prediction today. The experimentalists kindly provided us with the coordinates for T0288 ahead of time. We have started preliminary evaluation of models for this target and hopefully we will be able to determine one of the best models for it according to the GDT_TS score over the weekend. Then we will contact the author of this model and ask him/her for the permission for public release of the model. Then the model for the refinement will be posted at our web site and you will have approximately 3 more weeks to submit your refinement results as regular TS models with one adjustment - target name will need to be specified as TR288 (letter "R" instead of "0" in the target name). We will send you a reminder when the appropriate model is selected for refinement (likely early next week).
CASP6 participants might remember that in the previous round of our
experiment we asked predictors to submit multi-chain models for a target
that was specified by the the experimentalists as oligomeric. Last time
we got a very sparse response in this category and therefore, results
were not assessed. We decided to give another try to this initiative
this round of CASP. Target T0300 was specified by its supplier as a
dimer. This target is to expire in a week on June 16. Please, start
working on the dimeric model for this target if you plan to submit it
(obviously, this option is in ADDITION, not alternative, to the usual
CASP one-chain prediction).
Format requirements:
1. Only TS-type predictions will be accepted for oligomers.
2. Target record should be in the form
TARGET T0300 OLIGOMER
3. Each monomer should be identified as a separate chain, consecutive
capital letters for chain IDs should be used (in this case A and B).
4. Residue numbering in each chain starts from 1.
5. No TER or END records between monomers (chains).
Please, note that we are currently working on implementing details of
this format in our format verificators, so you won't be able to submit
oligomeric prediction over the weekend. We hope to have our system ready
for accepting this kind of predictions on Monday.
Today we received a question asking what is the procedure for submitting rankings of submitted models. Reminding that you can do this within the scope of our quality assessment category. Pick tarballs of all submitted 3D server models for a particular target at http://www2.predictioncenter.org/tarballs/ , run your quality evaluation software, assign each model a score and then report your data using the format http://predictioncenter.org/casp7/doc/casp7-format.html#QA . Please, be advised that data line in MODE 2 (residue-based error estimates) of your QA submission may be very long and then some editors/mailing programs may force line wrap potentially causing unexpected parsing errors. To avoid this problem we recommend that you split long lines into shorter sublines (50-100 columns of data) by yourself. Our parser will consider consecutive sublines (starting with the line containing evaluated model name and ending with the line containing the next model name or tag END) a part of the same logical line.
MODEL ACCURACY
We will pay special attention to model accuracy predictions. These can
be submitted for own predictions in the regular CASP format (PDB
B-factor field) on a per atom basis. These should be error estimates in
Angstroms. In addition an overall score for a given model can be
submitted as follows:
REMARK SCORE 0.7
in prediction header, where SCORE range is 0.0 to 1.0 (1.0 being a
perfect model). Independently, model accuracy predictions can be
submitted on server models, usually available within few days of target
release, or on your own models in the following format:
http://predictioncenter.org/casp7/doc/casp7-format.html#QA
The deadline for accuracy predictions on server models will be the
regular deadline for that target (typically 3 weeks).
In addition, to assess model evaluation methods on all CASP models
(i.e., including human expert predictions) we will be shorly collecting
software for a later assessment. Additional details will be announced
separately.
MODEL REFINEMENT
Special attention will also be paid to model refinement. In some cases
(CM/easy targets of less than 150 residues, preferably less than 100
residues), a single model submitted during the regular prediction window
will be selected for further refinement by others. Refinement window
will then open for additional 3 weeks. The usual refinement of own
models is still encouraged (using the unrefined and regular – for
refined models - model designations).
PREDICTION WINDOWS
Prediction windows will in general be shorter than in previous CASPs
(approximately 3 weeks). This is to adhere more closely to the
target structure release timelines adopted by crystallographers and to
minimize information leaks and subsequent target cancellations. However,
to allow assessment of methods requiring longer computation times, at
least some target deadlines will be extended. In such cases we will
still strongly encourage submitting models within the 3 week prediction
window. If information leak occurs after the initial three weeks but
before the assigned prediction deadline, evaluation of models will be
limited to those submitted within the 3 week window only.
PREDICTION OF FUNCTION
The format for function predictions is as follows:
http://predictioncenter.org/casp7/doc/casp7-format.html#FN
Additional targets will be made available for this category of
prediction (targets for which experimental structures may not be
forthcoming).
MODEL QUALITY FILTERS
Human expert predictions with severely unrealistic geometry will be
rejected outright. The criteria for this are as follows:
More than 5% of CAs taking part in clashes of less than 1.9 Angstrom.
OR
More than 25% of CAs taking part in clashes of less than 3.6 Angstrom.
CA-CA clashes below these percentage values as well as segmented
predictions with more than 4 chain breaks (CAs adjacent in sequence
separated by more than 5 Angstroms) will be flagged (warnings issued).
The model will be accepted, but it might be penalized in the assessment.
Missing loops or other deletions are acceptable.
Server predictions with clashes will be accepted in all cases, but
similarly to the human expert predictions will be issued warnings and
might be penalized in the assessment.
CASP7 organizers
Protein Structure Prediction Center