Sunday, December 25, 2005

The goal of MR-CAFASP, is to evaluate the potential of fully automatic 3D protein structure prediction servers to provide valuable models during the structure determination process.

During previous LiveBench experiments it was discovered that at least in two cases, highly confident "in-silico" models significantly differed from the experimental structure. In both cases, the experimental structure was subsequently removed from the PDB, and in one case, the replacement entry contained corrected models very similar to the original "in-silico" prediction (see e.g. Bujnicki et al, "Fold-Recognition Detects an Error in the Protein Data Bank.", Bioinformatics, 18, 1391-1395, 2002 and Bujnicki et al. "Errors in the D.radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools", FEBS letters, 525, 174-175, 2002 , and the crystallographers reply in the same issue). This lead to the question of whether in-silico models may be of help during the structure determination process - a very important issue for Structural Genomics.

This idea appeared in a previous CASP experiment, where predicted models were solicited for one target that could not be solved. In addition, D. Jones has also recently suggested that distant homology fold-recognition models may be used as Molecular Replacement phasing models (Jones, D. "Evaluating the potential of using fold-recognition models for molecular replacement.", Acta. Crys. D57, 1428-1434, 2001). D. Baker and colleagues have also described a method to generate structures using limited NMR data combined with in-silico procedures (Bowers, Strauss and Baker. J. Biomol. NMR, 18:311-318, 2000).