Classification and Recognition of Rossmann-Fold Protein

Abstract

Fold recognition is an important issue in protein structure research. The Rossmann-fold protein that has typical structure is a common kind of alpha/beta protein. The training set, selected from 22 families, is constituted of 79 Rossmann-fold proteins which have less than 25% sequence identity with each other. The hierarchical clustering method according to RMSD is applied and a profile-HMM based on structure alignment is built for each cluster. Testing on 9505 proteins with less than 95% sequence identity from Astral1.65, the sensitivity, specificity and MCC are 93.9%, 82.1% and 0.876 respectively. The result shows that building profile-HMMs after classification could reach precise fold recognition while a unified one cannot be built due to there are too many members in training set.