Protein structure optimization by side-chain positioning via beta-complex
DC Field | Value | Language |
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dc.contributor.author | Ryu, Joonghyun | - |
dc.contributor.author | Kim, Deok-Soo | - |
dc.date.accessioned | 2022-07-16T08:28:10Z | - |
dc.date.available | 2022-07-16T08:28:10Z | - |
dc.date.created | 2021-05-12 | - |
dc.date.issued | 2013-09 | - |
dc.identifier.issn | 0925-5001 | - |
dc.identifier.uri | https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/162042 | - |
dc.description.abstract | A molecular structure determines a molecular function(s) and a correct understanding of molecular structure is important for biotechnology. The computational prediction of molecular structure is a frequent requirement for important biomolecular applications such as a homology modeling, a docking simulation, a protein design, etc. where the optimization of molecular structure is fundamental. One of the core problems in the optimization of protein structure is the optimization of side-chains called the side-chain positioning problem. The side-chain positioning problem, assuming the rigidity of backbone and a rotamer library, attempts to optimally assign a rotamer to each residue so that the potential energy of protein is minimized in its entirety. The optimal solution approach using (mixed) integer linear programming, with the dead-end elimination technique, suffers even for moderate-sized proteins because the side-chain positioning problem is NP-hard. On the other hand, popular heuristic approaches focusing on speed produce solutions of low quality. This paper presents an efficient algorithm, called the BetaSCP, for the side-chain positioning problem based on the beta-complex which is a derivative geometric construct of the Voronoi diagram. Placing a higher priority on solution quality, the BetaSCP algorithm produces a solution very close to the optima within a reasonable computation time. The effectiveness and efficiency of the BetaSCP are experimentally shown via a benchmark test against well-known algorithms using twenty test models selected from Protein Data Bank. | - |
dc.language | 영어 | - |
dc.language.iso | en | - |
dc.publisher | SPRINGER | - |
dc.title | Protein structure optimization by side-chain positioning via beta-complex | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Kim, Deok-Soo | - |
dc.identifier.doi | 10.1007/s10898-012-9886-3 | - |
dc.identifier.scopusid | 2-s2.0-84884279352 | - |
dc.identifier.wosid | 000323741700009 | - |
dc.identifier.bibliographicCitation | JOURNAL OF GLOBAL OPTIMIZATION, v.57, no.1, pp.217 - 250 | - |
dc.relation.isPartOf | JOURNAL OF GLOBAL OPTIMIZATION | - |
dc.citation.title | JOURNAL OF GLOBAL OPTIMIZATION | - |
dc.citation.volume | 57 | - |
dc.citation.number | 1 | - |
dc.citation.startPage | 217 | - |
dc.citation.endPage | 250 | - |
dc.type.rims | ART | - |
dc.type.docType | Article; Proceedings Paper | - |
dc.description.journalClass | 1 | - |
dc.description.isOpenAccess | N | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Operations Research & Management Science | - |
dc.relation.journalResearchArea | Mathematics | - |
dc.relation.journalWebOfScienceCategory | Operations Research & Management Science | - |
dc.relation.journalWebOfScienceCategory | Mathematics, Applied | - |
dc.subject.keywordPlus | SEQUENCE SELECTION PROBLEM | - |
dc.subject.keywordPlus | VORONOI-DIAGRAM | - |
dc.subject.keywordPlus | DESIGN | - |
dc.subject.keywordPlus | PREDICTION | - |
dc.subject.keywordPlus | ALGORITHM | - |
dc.subject.keywordPlus | BACKBONE | - |
dc.subject.keywordPlus | CONFORMATIONS | - |
dc.subject.keywordPlus | TEMPLATES | - |
dc.subject.keywordPlus | FORMULATIONS | - |
dc.subject.keywordPlus | PREFERENCES | - |
dc.subject.keywordAuthor | Protein structure optimization | - |
dc.subject.keywordAuthor | Protein design | - |
dc.subject.keywordAuthor | Rotamer | - |
dc.subject.keywordAuthor | Voronoi diagram | - |
dc.subject.keywordAuthor | Quasi-triangulation | - |
dc.subject.keywordAuthor | Beta-complex | - |
dc.subject.keywordAuthor | Integer linear programming | - |
dc.subject.keywordAuthor | Optimal | - |
dc.subject.keywordAuthor | Heuristic | - |
dc.subject.keywordAuthor | BetaSCP | - |
dc.subject.keywordAuthor | SCWRL | - |
dc.subject.keywordAuthor | RASP | - |
dc.identifier.url | https://link.springer.com/article/10.1007%2Fs10898-012-9886-3 | - |
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