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

Joonghyun Ryu, Mokwon Lee, Jehyun Cha, Roman A. Laskowski, Seong Eon Ryu, Deok Soo Kim

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)W416-W423
JournalNucleic Acids Research
Volume44
Issue numberW1
DOIs
StatePublished - 2016 Jul 8

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Amino Acid Sequence
Proteins

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Ryu, Joonghyun ; Lee, Mokwon ; Cha, Jehyun ; Laskowski, Roman A. ; Ryu, Seong Eon ; Kim, Deok Soo. / BetaSCPWeb : side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization. In: Nucleic Acids Research. 2016 ; Vol. 44, No. W1. pp. W416-W423.
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BetaSCPWeb : side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization. / Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A.; Ryu, Seong Eon; Kim, Deok Soo.

In: Nucleic Acids Research, Vol. 44, No. W1, 08.07.2016, p. W416-W423.

Research output: Contribution to journalArticle

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AU - Kim, Deok Soo

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