BetaSuperposer: superposition of protein surfaces using beta-shapes
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Kim, Jae-Kwan | - |
dc.contributor.author | Kim, Deok-Soo | - |
dc.date.accessioned | 2022-07-16T14:35:24Z | - |
dc.date.available | 2022-07-16T14:35:24Z | - |
dc.date.created | 2021-05-12 | - |
dc.date.issued | 2012-07 | - |
dc.identifier.issn | 0739-1102 | - |
dc.identifier.uri | https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/165131 | - |
dc.description.abstract | The comparison between two protein structures is important for understanding a molecular function. In particular, the comparison of protein surfaces to measure their similarity provides another challenge useful for studying molecular evolution, docking, and drug design. This paper presents an algorithm, called the BetaSuperposer, which evaluates the similarity between the surfaces of two structures using the beta-shape which is a geometric structure derived from the Voronoi diagram of molecule. The algorithm performs iterations of mix-and-match between the beta-shapes of two structures for the optimal superposition from which a similarity measure is computed, where each mix-and-match step attempts to solve an NP-hard problem. The devised heuristic algorithm based on the assignment problem formulation quickly produces a good superposition and an assessment of similarity. The BetaSuperposer was fully implemented and benchmarked against popular programs, the Dali and the Click, using the SCOP models. The BetaSuperposer is freely available to the public from the Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr). | - |
dc.language | 영어 | - |
dc.language.iso | en | - |
dc.publisher | TAYLOR & FRANCIS INC | - |
dc.title | BetaSuperposer: superposition of protein surfaces using beta-shapes | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Kim, Deok-Soo | - |
dc.identifier.doi | 10.1080/07391102.2012.689700 | - |
dc.identifier.scopusid | 2-s2.0-84871252063 | - |
dc.identifier.wosid | 000309124500006 | - |
dc.identifier.bibliographicCitation | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, v.30, no.6, pp.684 - 700 | - |
dc.relation.isPartOf | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS | - |
dc.citation.title | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS | - |
dc.citation.volume | 30 | - |
dc.citation.number | 6 | - |
dc.citation.startPage | 684 | - |
dc.citation.endPage | 700 | - |
dc.type.rims | ART | - |
dc.type.docType | Article | - |
dc.description.journalClass | 1 | - |
dc.description.isOpenAccess | N | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Biochemistry & Molecular Biology | - |
dc.relation.journalResearchArea | Biophysics | - |
dc.relation.journalWebOfScienceCategory | Biochemistry & Molecular Biology | - |
dc.relation.journalWebOfScienceCategory | Biophysics | - |
dc.subject.keywordPlus | STRUCTURE ALIGNMENT | - |
dc.subject.keywordPlus | DISTANCE MATRICES | - |
dc.subject.keywordPlus | VORONOI-DIAGRAM | - |
dc.subject.keywordPlus | SEQUENCE | - |
dc.subject.keywordPlus | SIMILARITIES | - |
dc.subject.keywordPlus | DATABASE | - |
dc.subject.keywordPlus | SCOP | - |
dc.subject.keywordPlus | TRANSFORMATIONS | - |
dc.subject.keywordPlus | CLASSIFICATION | - |
dc.subject.keywordPlus | SITES | - |
dc.subject.keywordAuthor | molecule structure | - |
dc.subject.keywordAuthor | molecule superposition | - |
dc.subject.keywordAuthor | molecule structure alignment | - |
dc.subject.keywordAuthor | Voronoi diagram | - |
dc.subject.keywordAuthor | beta-complex | - |
dc.subject.keywordAuthor | beta-shape | - |
dc.subject.keywordAuthor | PDB | - |
dc.identifier.url | https://www.tandfonline.com/doi/full/10.1080/07391102.2012.689700 | - |
Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.
222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Korea+82-2-2220-1365
COPYRIGHT © 2021 HANYANG UNIVERSITY.
Certain data included herein are derived from the © Web of Science of Clarivate Analytics. All rights reserved.
You may not copy or re-distribute this material in whole or in part without the prior written consent of Clarivate Analytics.