Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL

We present results of comparative modeling on 11 targets from the CASP3 experiment. Our methods comprise the following steps: first, PSI-BLAST is used to find homologues of the target sequence in the nonredundant GenBank protein sequence database; second, after several iterations of PSI-BLAST, the resulting profile or position-specific similarity matrix is used to search a database of Protein Databank (PDB) sequences; third, from the list of hits resulting from the PDB search, a parent structure is chosen on the basis of the quality of the alignment and the quality of the experimental structure; fourth, this alignment is adjusted manually whenever insertions or deletions take place in secondary structure regions of the parent; fifth, the backbone is modeled from the parent structure and the alignment; and finally, the program SCWRL is used to replace nonconserved side chains onto the parent backbone given the target sequence. For comparison, we also produced structural models from the unaltered PSI-BLAST alignment, from an alignment from the nonprofile version of BLAST, and from the global sequence alignment program CLUSTAL W. Our results indicate that PSI-BLAST produced considerably better alignments than would be possible with either global or local pairwise sequence alignment algorithms and that manual adjustments were helpful. SCWRL, which uses a backbone-dependent rotamer library to predict side-chain conformations, did well in comparison with other methods used in CASP3.