A beta-complex statistical four body contact potential combined with a hydrogen bond statistical potential recognizes the correct native structure from protein decoy sets
DC Field | Value | Language |
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dc.contributor.author | Sanchez-Gonzalez, Gilberto | - |
dc.contributor.author | Kim, Jae-Kwan | - |
dc.contributor.author | Kim, Deok-Soo | - |
dc.contributor.author | Garduno-Juarez, Ramon | - |
dc.date.accessioned | 2022-07-16T08:48:36Z | - |
dc.date.available | 2022-07-16T08:48:36Z | - |
dc.date.created | 2021-05-12 | - |
dc.date.issued | 2013-08 | - |
dc.identifier.issn | 0887-3585 | - |
dc.identifier.uri | https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/162265 | - |
dc.description.abstract | We present a new four-body knowledge-based potential for recognizing the native state of proteins from their misfolded states. This potential was extracted from a large set of protein structures determined by X-ray crystallography using BetaMol, a software based on the recent theory of the beta-complex (-complex) and quasi-triangulation of the Voronoi diagram of spheres. This geometric construct reflects the size difference among atoms in their full Euclidean metric; property not accounted for in a typical 3D Delaunay triangulation. The ability of this potential to identify the native conformation over a large set of decoys was evaluated. Experiments show that this potential outperforms a potential constructed with a classical Delaunay triangulation in decoy discrimination tests. The addition of a statistical hydrogen bond potential to our four-body potential allows a significant improvement in the decoy discrimination, in such a way that we are able to predict successfully the native structure in 90% of cases. Proteins 2013; 81:1420-1433. | - |
dc.language | 영어 | - |
dc.language.iso | en | - |
dc.publisher | WILEY | - |
dc.title | A beta-complex statistical four body contact potential combined with a hydrogen bond statistical potential recognizes the correct native structure from protein decoy sets | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Kim, Deok-Soo | - |
dc.identifier.doi | 10.1002/prot.24293 | - |
dc.identifier.scopusid | 2-s2.0-84880703979 | - |
dc.identifier.wosid | 000329220400012 | - |
dc.identifier.bibliographicCitation | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v.81, no.8, pp.1420 - 1433 | - |
dc.relation.isPartOf | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | - |
dc.citation.title | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | - |
dc.citation.volume | 81 | - |
dc.citation.number | 8 | - |
dc.citation.startPage | 1420 | - |
dc.citation.endPage | 1433 | - |
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 | MEAN FORCE | - |
dc.subject.keywordPlus | DEPENDENT CONTRIBUTIONS | - |
dc.subject.keywordPlus | DELAUNAY TESSELLATION | - |
dc.subject.keywordPlus | RESIDUE POTENTIALS | - |
dc.subject.keywordPlus | PAIR POTENTIALS | - |
dc.subject.keywordPlus | ENERGY FUNCTION | - |
dc.subject.keywordPlus | IDENTIFICATION | - |
dc.subject.keywordPlus | PREDICTION | - |
dc.subject.keywordPlus | VORONOI | - |
dc.subject.keywordAuthor | beta-complex theory | - |
dc.subject.keywordAuthor | energy potentials | - |
dc.subject.keywordAuthor | four-body statistical potential | - |
dc.subject.keywordAuthor | hydrogen bond statistical potential | - |
dc.subject.keywordAuthor | improvement of decoy discrimination | - |
dc.subject.keywordAuthor | protein structure prediction | - |
dc.identifier.url | https://onlinelibrary.wiley.com/doi/10.1002/prot.24293 | - |
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