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.
CASP9 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.
- Prediction of
multimeric structures will be reinstated in CASP9.
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).
Note.
Domain boundary prediction category has been dropped from
CASP9.
There will be additional activities included in or related to CASP9,
which extend its scope.
SAC-CASP9:
We plan that CASP9 meeting will be joined
by the Student Addendum Conference. SAC-CASP9 will use the same
conference facilities as CASP9. It will start (tentatively) the day
after CASP9 and will last one day. Details about this Conference will
be announced later.
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
2010.
Testing of server connectivity ("dry run" for server predictors) will
be conducted starting April 14. The first prediction targets will be
released not earlier than May 3; 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 20.
Abstracts describing the methods tested in CASP9 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 5-9, and approximately one
month before that groups with the most accurate and interesting
predictions 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
CASP9 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 CASP9. 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, 2010. The last day for suggesting
proteins as CASP targets is July 16, 2010.
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 CASP9 will be split in two prediction tracks: 1) human/server
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 human-expert modeling experiment 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 human-expert
groups. All targets are assigned two expiration dates (one - for server predictors
and another - for human-expert 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 human/server
track and as many targets as we can get in the server-only track.
The human-expert 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 human-expert groups will be placed on the selected targets.
Note, that distinction between the human/server and server-only targets
pertains to the tertiary/quaternary structure predictions only. In other
prediction categories (DR/RR/FN/QA), all groups (including human-expert)
are expected to submit their predictions on all targets.
Predictions in
CASP format
must be submitted to this web site or through the email. For 3D coordinate
predictions, this is a simple PDB-like file with consecutive
numbering of residues 1 -> N and a small number of required
headers.
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 -
Torsten Schwede (University of Basel, Switzerland)
-
Template free modeling -
Nick Grishin (University of Texas, USA)
-
Refinement and physics-based prediction methods -
Ken Dill (University of California, San Francisco, USA)
Other prediction categories (contacts, binding sites, disorder, quality assessment)
will be evaluated by the selected assessors and the organizers.
Click here
for the list of assessors in all CASPs held so far.
In accordance with CASP policy, assessors are not directly
involved in the organization of the experiment, nor can they take part
in the experiment as predictors. Predictors must not
contact assessors directly with queries, but rather these should be
sent to the
email
address.
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 Asilomar Conference Center,
Pacific Grove, California on December 5-9, 2010 (starting at 6pm on the 5th and ending at 12pm on the 9th). Program of the meeting will be available in mid-November. The
meeting will have limited attendance (about 200 participants)
and precedence will be given to active predictors.
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
Anna Tramontano, University of Rome, Italy
David Baker, University of Washington
Phil Bourne, University of California, San Diego and RCSB
David Jones, University College, London
Roland Dunbrack, Fox Chase Cancer Center
BK Lee, National Institutes of Health
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