OPUS-Beta: A Statistical Potential for Beta-Sheet Contact Pattern in Proteins

Abstract: Developing an accurate scoring function is essential for successfully predicting protein structures. In this study, we developed a statistical potential function, called OPUS-Beta, for energetically evaluating beta-sheet contact pattern (the entire residue-residue beta-contacts of a protein) independent of the atomic coordinate information. The OPUS-Beta potential contains five terms, i.e., a self-packing term, a pairwise inter-strand packing term, a pairwise intra-strand packing term, a lattice term and a hydrogen-bonding term. The results show that, in recognizing the native beta-contact pattern from decoys, OPUS-Beta potential outperforms the existing methods in literature, especially in combination with a method using 2D-recursive neural networks (about 5% and 23% improvements in top-1 and top-5 selections). We expect OPUS-Beta potential to be useful in beta-sheet modeling for proteins.