A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

Abstract

RW and RWplus demonstrate a significantly better ability than the best performing pair-wise distance-dependent atomic potential functions in both native and near-native model selections. It has higher energy-RMSD and energy-TM-score correlations compared with other potentials of the same type in real-life structure assembly decoys. When benchmarked with a comprehensive list of publicly available potentials, RW and RWplus shows comparable performance to the state-of-the-art scoring functions, including those combining terms from multiple resources. These data demonstrate the usefulness of random-walk chain as reference states which correctly account for sequence connectivity and entropic elasticity of proteins. It shows potential usefulness in structure recognition and protein folding simulations. The RW and RWplus potentials, as well as the newly generated I-TASSER decoys, are freely available in http://zhanglab.ccmb.med.umich.edu/RW.