Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure

Analysis of our fold recognition results in the 3rd Critical Assessment in Structure Prediction (CASP3) experiment, using the programs THREADER 2 and GenTHREADER, shows an encouraging level of overall success. Of the 23 submi tted predictions, 20 targets showed no clear sequence similarity to protein s of known 3D structure. These 20 targets can be divided into 22 domains, o f which, 20 domains either entirely match a previously known fold, or parti ally match a substantial region of a known fold. Of these 20 domains, we co rrectly assigned the folds in 10 cases. (C) 1999 Wiley-Liss, Inc.