MODEL-BUILDING BY COMPARISON - A COMBINATION OF EXPERT KNOWLEDGE AND COMPUTER AUTOMATION

The CASP blind trials (Critical Assessment of techniques for protein S tructure Prediction) assess the accuracy of protein prediction that in cludes evaluation of comparative model building of protein structures. Comparative models of four proteins (T0001, T0003, T0017, and T0028) for CASP2 (held during 1996) were constructed using computer algorithm s combined with visual inspection, Essentially the main-chain modellin g involves construction of the target structure from rigid-body segmen ts of homologues and loop fragments extracted from homologous and nonr edundant databases, Side-chains were initially constructed by inherita nce from the parent or from a rotamer library, Side-chain conformation s were then refined using a novel mean field approach that includes so lvation, Comparison of the models with the subsequently released X-ray structures identified the successes and limitations of our approach. The most problematic area is the quality of the sequence alignments be tween parent(s) and target, In this respect the overinterpretation of the conserved features within homologous families can be misleading, S everal features of our approach have a positive effect on the accuracy of the models, For T0003, inspection correctly identified that a lowe r sequence identity parent provides the best framework for this model, Loop selection worked well where a homologous protein fragment was us ed, but that the use of nonredundant fragment library remains problema tic for hinge movements and displacements in secondary structure eleme nts relative to the parent, Side-chain refinement improved residue con formations relative to the initial model, Use of limited energy minimi zation improved the stereochemical quality of the model without increa sing the RMS deviation, This study has identified methods that are eff ective and areas requiring further attention to improve model building by comparison. (C) 1998 Wiley-Liss, Inc.