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 p...

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Detalles Bibliográficos
Autores principales: Ryu, Joonghyun, Lee, Mokwon, Cha, Jehyun, Laskowski, Roman A., Ryu, Seong Eon, Kim, Deok-Soo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Web Server issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987919/
https://www.ncbi.nlm.nih.gov/pubmed/27151195
http://dx.doi.org/10.1093/nar/gkw368
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author Ryu, Joonghyun
Lee, Mokwon
Cha, Jehyun
Laskowski, Roman A.
Ryu, Seong Eon
Kim, Deok-Soo
author_facet Ryu, Joonghyun
Lee, Mokwon
Cha, Jehyun
Laskowski, Roman A.
Ryu, Seong Eon
Kim, Deok-Soo
author_sort Ryu, Joonghyun
collection PubMed
description 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.
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spelling pubmed-49879192016-08-22 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 Nucleic Acids Res Web Server issue 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. Oxford University Press 2016-07-08 2016-05-05 /pmc/articles/PMC4987919/ /pubmed/27151195 http://dx.doi.org/10.1093/nar/gkw368 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server issue
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
title BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization
title_full BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization
title_fullStr BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization
title_full_unstemmed BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization
title_short BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization
title_sort betascpweb: side-chain prediction for protein structures using voronoi diagrams and geometry prioritization
topic Web Server issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987919/
https://www.ncbi.nlm.nih.gov/pubmed/27151195
http://dx.doi.org/10.1093/nar/gkw368
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