Description of the experiment
The main goal of CASP is to obtain an in-depth and objective assessment
of our current
abilities and inabilities in the area of protein structure prediction.
To this end, participants will predict as much as possible about a set
of soon to be known
structures. These will be true predictions, not ‘post-dictions’ made on
already known structures.
CASP10 will particularly address the following questions:
-
Are the models produced similar to the corresponding experimental
structure?
- Is the mapping of the target sequence onto the proposed
structure
(i.e. the alignment) correct?
- Have similar structures that a model can be based on been
identified?
- Are comparative models more accurate than can be obtained
by simply
copying the best template?
- Has there been progress from the earlier CASPs?
- What methods are most effective?
- Where can future effort be most productively focused?
Tertiary structure predictions (TS):
- The 'Template
based modeling' category will include domains where a
suitable template can be identified that covers all or nearly all of
the target.
- The 'Template
free modeling' category will include models of proteins
for which no suitable template can be identified.
- Detailed analysis of
the side chains, loops, and active sites will be performed for those
structure models where the backbone is sufficiently accurate.
- Success in refining models beyond the quality obtained by
simply copying from a single template will be analyzed. We
will select a subset of targets from among the best
models received during the prediction season, and these best models
will be reissued as starting structures for refinement.
Other prediction categories:
- Detecting residue-residue contacts in proteins (RR).
- Identifying disordered regions in target proteins (DR).
- Function prediction (prediction of binding sites) (FN).
- Quality assessment of models in general (without
knowing native structures) and the reliability of predicting certain
residues in particular (QA).
There will be additional activities included in or related to CASP10,
which extend its scope.
Rolling CASP:
We will discuss the results of the Rolling CASP experiment
at the CASP10 predictors' meeting.
FORCASP:
There will be discussion of predictions and methods
on our
FORCASP forum.
Registration for the experiment will start in the last week of March
2012.
Testing of server connectivity ("dry run" for server predictors) will
be conducted starting April 16, 2012. The first prediction targets will be
released not earlier than May 1; the last prediction targets will be
released not later than July 17; prediction season will end not later
than July 31. Refinement experiment will end not later than August 17.
Abstracts describing the methods tested in CASP10 will be collected in
September. At the same time we will open registration for the meeting.
The program of the meeting will be available in November.
The meeting will take place on December 9-12, and approximately one
month before that groups with the most accurate predictions and interesting
methods will receive invitations to give talks.
Participation is open to all. If you already have an account with the
Prediction Center, you will be able to go directly to the
CASP10 registration page.
Please check, though, that you basic registration information is
current. If it has changed - please update it through the My Personal
Data link from the main Menu. If you are new to CASP and don't
have
an account with us, you will have to register with the Prediction
Center first, and only then - for CASP10. Separate registration forms
for different types of registration will be available through this
website. Predictors with servers are requested to register as soon as
the registration page is available as we are planning on starting a
"dry run" for servers in the second decade of April.
For the experiment to succeed, it is essential that we obtain the help
of the experimental
community. As in previous CASPs, we invite protein crystallographers and NMR
spectroscopists to provide details of structures they expect to have
made public before September 10, 2012. The last day for suggesting
proteins as CASP targets is July 16, 2012.
During the prediction season, targets are being posted daily at the
Target List page
and, additionally, automatically pushed to the
registered prediction servers.
Targets in CASP10 will be split in two prediction tracks: 1) regular
and 2) server only. Assignment of the target to a particular track is
made by the organizers and communicated to the predictors through the
Target List page. Subject to the availability, priority for inclusion in
the regular modeling track will be given to targets containing
low homology domains.
Targets are planned to be released on business days only, around 9am PDT.
Requests to the participating servers will be sent immediately after the
target release through the web page. We plan to release not more than 3
targets per day for servers and, usually, one target per day for all
groups. All targets are assigned two expiration dates (one - for server predictors
and another - for regular groups), and predictions must be received
and accepted before noon, 12pm PDT on the corresponding expiration date.
We are planning to release 50-60 targets for evaluation in the regular (late deadline)
track and as many targets as we can get in the server-only track.
The regular groups wishing to take the challenge
and predict structures for all of the released targets (including the
"server-only" ones) are welcome to do so but the evaluation accent for
the regular groups will be placed on the selected targets.
Note, that distinction between the regular and server-only targets
pertains to the tertiary/quaternary structure predictions only. In other
prediction categories (DR/RR/FN/QA), all groups
are expected to submit their predictions on all targets.
Predictions
must be submitted through the Prediction Submission form on this web site
or by the email.
As in previous CASPs, independent assessors will evaluate the
predictions.
Assessors will be provided with the results of numerical prediction evaluations performed at the
Prediction Center, and will judge the results primarily on that basis.
They will be asked to focus particularly on the effectiveness of different methods.
Evaluation criteria will as far as possible be similar to those used in previous CASPs,
although the assessors are welcome to introduce additional measures.
There will be three assessors, focusing on the following areas of prediction:
-
Template based modeling -
TBA
-
Template free modeling -
TBA
-
Refinement and physics-based prediction methods -
TBA
Other prediction categories (contacts, binding sites, disorder, quality assessment)
will be evaluated by the selected assessors and the organizers.
The list of CASP10 assessors will be posted here in the beginning of the year 2012.
All CASP predictions and results of numerical evaluation will be made available through
this web site shortly before the meeting.
The proceedings of the meeting will be published in a scientific journal (see publications of previous experiments).
All participants will also be required to describe their methods
in the abstracts (published locally at our web site) and encouraged to
discuss them on the
FORCASP forum.
These contributions will be discussed and scored
by other predictors, and this material 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.
The meeting to discuss results of the experiment will be held
at the Hotel Serapo in
Gaeta (Italy)
on December 9-12, 2012 (starting at 6pm on the 9th and ending in the
afternoon of the 12th).
Program of the meeting will be available in mid-November, 2012.
Some financial assistance will be available for the most successful
predictors and students.
John Moult, CASP president; CARB, University of Maryland, USA
Krzysztof Fidelis, University of California, Davis, USA
Andriy Kryshtafovych, University of California, Davis, USA
Torsten Schwede, University of Basel, Switzerland
Anna Tramontano, University of Rome, Italy
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