BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement.Hanyang University [HY-2012 to J.R., D.-S.K.]; National Research Foundation of Korea (Basic Science Research Program) [2015R1D1A1A01061361 to J.R., M.L., J.C., D.S.K.]; National Research Foundation of Korea (Biomedical technology development) [2015M3A9B5029741 to S.E.R.]