PREDICTION OF PROTEIN SIDE-CHAIN CONFORMATIONS BY PRINCIPAL COMPONENTANALYSIS FOR FIXED MAIN-CHAIN ATOMS

A method of side-chain prediction without calculating the potential fu nction is introduced. It is based on the assumption that similar side- chain conformations have a similar structural environment around the s ide chains. The environment information is represented by vectors that were obtained from principle component analysis and represented by th e variance of positions of main-chain atoms around side chains. This i nformation was added to the side-chain library (rotamer library) made from Xray structures. Side-chain conformations were constructed using this side-chain library without using potential functions. An optimal solution was determined by comparing environmental information with th e backbone conformation around the side chain to be predicted and nati ve ones in the library. The method was performed for 15 proteins whose structures were known. The result for the root-mean-square deviation between the predicted and X-ray side-chain conformations was similar t o 1.5 Angstrom (the value for core residues was similar to 1.1 Angstro m) and the percentage of predicted chi(1) angles correct within 40 deg rees was similar to 65% (75% for the core). The computational time was short (similar to 60 s for the prediction of proteins with 200 amino acid residues). About 70% of the side-chain conformations were constru cted by location of the main-chain atoms around the central C-beta ato m and the average of r.m.s.d. was similar to 1.4 Angstrom (for core re sidues the average was similar to 1.0 Angstrom).