Search for the most stable folds of protein chains: III. Improvement in fold recognition by averaging over homologous sequences and 3D structures

Three-dimensional (3D) protein gives fold recognition by query sequence can be improved using information of fold recognition yielded by the sequences homologous to the query one. This idea is now used more and more widely, O ur paper presents its consequent development. We suggest incorporating info rmation both on the sequences homologous to the query protein sequence and the 3D structures homologous to the target (already deciphered) protein fol ds. We show that both these tricks, and especially their combination reduce s errors in fold recognition by the threading method. Proteins 2000;40:494- 501. (C) 2000 Wiley-Liss, Inc.