CASP 10: Call for targets to assess the
state of the art in protein structure modeling
As many of you know, CASP (Critical Assessment of Structure
prediction) has been assessing the state of the art in modeling
protein structure from sequence since 1994, running a community
experiment once every two years. In these experiments, information
on soon to be solved structures is collected from the experimental
community, and the sequence data are passed to the structure
modeling community so that blind predictions of structure and can
collected and assessed (1). Over that period CASP has seen enormous
progress in the quality of modeled structures (2), but many problems
remain. CASP is only possible because of the generous participation
of the experimental community in providing the modeling targets (3).
We recently appealed for your help in providing novel fold and
membrane protein targets for the ongoing CASP ROLL process. That is
very successful, with 57 prediction teams participating and 26
targets already released, thanks to all of you who have contributed.
The prediction season for the next full biannual experiment, CASP
10, begins May 1, and so we are now asking for your help again, this
time in reaching our goal of releasing at least varied 100 targets
in a the three-month period. We need all sorts of targets, spanning
the categories below:
1. (More than ever) novel folds and membrane protein targets – even
with the extended collection season provided by CASP ROLL, there
will be still a shortage. There are some interesting methods
developments for ab initio modeling, and it is important to be able
to decisively evaluate their effectiveness.
2. A diversity of comparative modeling targets. Cases where the
there is fairly high sequence identity (30-50%) between the target
structure and an available template are valuable for testing the
degree to which model accuracy can approach that of experiment,
particularly in functionally critical regions. Cases with lower
sequence identity to template, right down to undetectable, are
valuable for testing the ability of the methods to detect remote
homologs, to overcome challenging alignment difficulties, to make
use of multiple templates, and to build regions of the structure not
obviously available from a template.
3. Targets containing significant amounts of disordered structure,
so as to test the ability of methods to identify these regions.
Disorder identified by absence of density in crystallography is
current the main source and very useful, but its important to have
cases where the nature of the disorder has been established by other
means, such as NMR.
4. Some targets will also be used to test methods of structure
refinement. In these cases, the best model received for a target
will be released to the refinement community, who will subsequently
submit new models. This too is an area where there have been some
exciting developments in the last year, so we are hoping for
significant progress. Refinement targets are selected based on the
nature of the errors in the initial models. Because of the extended
process, these targets need to be available for longer before
release of the experimental structure.
For those of you who have not provided targets to CASP before, the
procedure is simple. There are three ways to submit targets: (1) Go
the target submission web page and fill in the easy form; (2) When
you submit your co-ordinates to the PDB, tick the ‘CASP HOLD’ box,
automatically setting up a target entry; (3) Send an email the
prediction center with details. If you have queries, there is a very
experienced prediction center staff to deal with them. The key thing
is timing: We need a window of at least four weeks between receiving
information about a target and the release of your experimental
structure. A longer window – up to eight weeks - is often useful,
for example so that a target can be used to test refinement methods,
but is not essential (note that using the PDB target submission
route automatically selects eight weeks). We don’t need your
experimental structure in advance of its release by the PDB,
provided that will happen by the end of August. Please consult the
target submission page for more details: http://www.predictioncenter.org/casp10/targets_submission.cgi
There are already over 200 prediction teams signed for CASP 10, and
so any targets provided will receive plenty of attention. If you
have a suitable target now, we are ready to receive it. If new
targets come up before July 17, we would also love to have them.
(After July 17, we will continue with CASP ROLL for novel folds and
membrane proteins). So please get in touch whenever a suitable
opportunity arises, and help improve modeling methods.
Thanks,
CASP organizing committee
John Moult, IBBR, University of Maryland, USA
Krzysztof Fidelis, University of California, Davis, USA
Andriy Kryshtafovych, University of California, Davis, USA
Torsten Schwede, SIB & Biozentrum University of Basel,
Switzerland
Anna Tramontano, University of Rome, Italy
Get in touch: [log in to unmask]
More information: http://www.predictioncenter.org/casp10/index.cgi
CASP Roll targets so far: http://www.predictioncenter.org/casprol/targetlist.cgi
Submit a target: http://www.predictioncenter.org/casp10/targets_submission.cgi
1. Critical
assessment of methods of protein structure prediction
(CASP)--round IX.
Moult J, Fidelis K, Kryshtafovych A, Tramontano A.
Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200. Epub 2011
Oct 14.
2. CASP9
results compared to those of previous CASP experiments.
Kryshtafovych A, Fidelis K, Moult J.
Proteins. 2011;79 Suppl 10:196-207. doi: 10.1002/prot.23182. Epub
2011 Oct 14
3. Target
highlights in CASP9: Experimental target structures for the
critical assessment of techniques for protein structure
prediction.
Kryshtafovych A et al.
Proteins 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011
Oct 21.
