Analysis of comparative modeling predictions for CASP2 targets 1, 3, 9, and 17

Comparative modeling targets 1, 3, 9 and 17 were predicted by alignment of multiple sequences and structures, when available, followed by minimization using the program AMMP. The minimization used improved potentials, and distance restraints for regions of common structure. New prediction procedures were evaluated. Three tested solvent corrections did not significantly improve the predictions. Target 17 had 85.3% sequence identity with the parent and no insertions or deletions. The prediction had a root-mean-square deviation from target 17 of 0.56 A on C alpha atoms, and 0.59 A for the ligand atoms, which verified the accuracy of the minimization. Targets 1, 3, and 9 had 36.4%, 46.7%, and 33.3% identity with the parent sequences, and predictions resulted in root-mean-square deviations for 79-85% of C alpha atoms of 1.49, 1.11, and 1.24 A, respectively. Conformational differences between parent and target crystal structures were difficult to predict. The use of distance restraints and multiple structures improved the positioning of gaps in sequence alignment. Distance restraints did not overcome errors in sequence alignment or ambiguities due to conformational variation in proteins. Predictions for targets 3 and 9 successfully reduced large deviations between parent and target structures.