HANDLING CONTEXT-SENSITIVITY IN PROTEIN STRUCTURES USING GRAPH-THEORY- BONA-FIDE PREDICTION

We constructed five comparative models in a blind manner for the secon d meeting on the Critical Assessment of protein Structure Prediction m ethods (CASP2). The method used is based on a novel graph-theoretic cl ique-finding approach, and attempts to address the problem of intercon nected structural changes in the comparative modeling of protein struc tures. We discuss briefly how the method is used for protein structure prediction, and detail how it performs in the blind tests, We find th at compared to CASP1, significant improvements in building insertions and deletions and sidechain conformations have been achieved. (C) 1998 Wiley-Liss, inc.