CASP Roll: Call for novel fold and membrane protein targets to help improve structure modeling methods

From: Torsten Schwede
Date: 6 February 2012 22:29


Dear colleagues,

As many of you know, the CASP community experiments have been running once every two years since 1994, collecting information on soon to be solved structures from the experimental community, and passing on sequence data to the structure modeling community so that blind predictions of structure can be collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. The regular CASP experiments collect target information for a three month season every two years, and in that period, thanks especially to the structural genomics community, can acquire over 100 targets, sufficient to evaluate the state of the art for most types of template based modeling.

There are some classes of target, specifically proteins with novel folds and membrane proteins, where there are not enough structures solved in three months to provide sufficient information so the methods can be fully evaluated. As a consequence, progress is slowed. To address this problem, with the encouragement of the modeling community, CASP has launched a rolling mechanism, where we accept targets in these categories at any time. Of course for that to work we rely on you, the experimentalists, to provide suitable targets! So we are asking that you tell us about structures in these categories that are about to be solved whenever they come up.

For those of you who have not provided targets to CASP before, the procedure is simple – there is a web page for submitting targets, and a very experienced staff to deal with any queries. We don't need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release.

If you have a suitable target now, we are up and running with 50+ prediction teams already submitting models, and would love to have your targets. Most important, the modeling community is now in continuous need of your assistance, so please get in touch whenever an opportunity arises in the future, 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, University of Basel & SIB, Switzerland
Anna Tramontano, University of Rome, Italy


More information: http://www.predictioncenter.org/casprol/
CASP Roll targets so far: http://www.predictioncenter.org/casprol/targetlist.cgi
Submit a target: http://www.predictioncenter.org/casprol/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.