title: BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.
abstract: 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.
authors.affiliation: Vorononi Diagram Research Center, Hanyang University, Korea.
authors.forename: Joonghyun
authors.initials: J
authors.lastname: Ryu
authors.affiliation: Vorononi Diagram Research Center, Hanyang University, Korea.
authors.forename: Mokwon
authors.initials: M
authors.lastname: Lee
authors.affiliation: Vorononi Diagram Research Center, Hanyang University, Korea.
authors.forename: Jehyun
authors.initials: J
authors.lastname: Cha
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, UK.
authors.forename: Roman A
authors.initials: RA
authors.lastname: Laskowski
authors.affiliation: Department of Bioengineering, Hanyang University, Korea.
authors.forename: Seong Eon
authors.initials: SE
authors.lastname: Ryu
authors.affiliation: School of Mechanical Engineering, Hanyang University, Korea dskim@hanyang.ac.kr.
authors.forename: Deok-Soo
authors.initials: DS
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D020407:Internet; D008433:Mathematics; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013816:Thermodynamics
chemical_list: D011506:Proteins