Fifth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction

The CAFASP/CASP Interaction

As noted before, all CAFASP server predictions will be also considered part of CASP. Thus, the server predictions will undergo two separate, independent evaluations. The first will be carried out automatically by the CAFASP procedures, as described before. The second will be carried out by the CASP assessors. This will enable a direct comparison between the predictions filed by servers and those filed by human CASP predictors. Because the two experiments are so closely linked, no server prediction will be accepted by CASP if it is not accepted by CAFASP, and no server prediction will be accepted by CAFASP if it is not accepted by CASP.

To facilitate the interaction between the two experiments, in addition to having the servers coupled to the CAFASP meta-server, CAFASP server-developers are required to register their servers at CASP, as servers at: http://PredictionCenter.llnl.gov/casp5/predictors/forms/casp5-reg-ser.html (note that this is not the same registration as required for non-server participation in CASP). The resulting registration code will be the means to identify each server in the CASP evaluation. Only servers both registered at CASP as servers, and coupled to the CAFASP meta-server will be considered.

The final form of all CAFASP meta-server collected predictions will be forwarded to CASP. Thus, all conversions performed by CAFASP, for example from alignments to co-ordinates, will be the input to CASP. Note that, unlike in CAFASP2, server developers do not send initial submissions directly to CASP.

All server predictions will be converted to full CASP format once received by CASP. Server developers will be notified directly when a prediction has been processed by CASP, either with a standard acceptance message, or with an error message. Wherever possible, CASP will accept revised predictions, with corrected errors, provided these do not alter the substance of a prediction. If a prediction is not accepted by CASP, and the server developer fails to correct the file, then this prediction will be removed from CAFASP. Since the finalization of CAFASP files may take up to two weeks, it may be up to that period after a CAFASP target deadline before server developers receive the CASP message.

To ease CASP compatibility problems, servers in the Homologous Modeling and 'Ab Initio' CAFASP categories are asked to make sure that their PDB output is CASP readable.

CASP and CAFASP organizers

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