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.
Nucleic Acids Res.