Ligand Aligning Method for Molecular Docking: Alignment of Property-Weighted Vectors
DC Field | Value | Language |
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dc.contributor.author | Joung, Jong Young | - |
dc.contributor.author | Nam, Ky-Youb | - |
dc.contributor.author | Cho, Kwang-Hwi | - |
dc.contributor.author | No, Kyoung Tai | - |
dc.date.available | 2018-05-10T05:25:18Z | - |
dc.date.created | 2018-04-17 | - |
dc.date.issued | 2012-04 | - |
dc.identifier.issn | 1549-9596 | - |
dc.identifier.uri | http://scholarworks.bwise.kr/ssu/handle/2018.sw.ssu/12468 | - |
dc.description.abstract | To reduce searching effort in conformational space of ligand docking positions, we propose an algorithm that generates initial binding positions of the ligand in a target protein, based on the property-weighted vector (P-weiV), the three-dimensional orthogonal vector determined by the molecular property of hydration-free energy density. The alignment of individual P-weiVs calculated separately for the ligand and the protein gives the initial orientation of a given ligand conformation relative to an active site; these initial orientations are then ranked by simple energy functions, including solvation, Because we are using three-dimensional orthogonal vectors to be aligned, only four orientations of ligand positions are possible for each ligand conformation, which reduces the search space dramatically. We found that the performance of P-weiV compared favorably to the use of principle moment of inertia (PMI) as implemented in LigandFit when we tested the abilities of the two approaches to correctly predict 205 protein-ligand complex data sets from the PDBBind database. P-weiV correctly predicted the alignment of ligands (within rmsd of 2.5 angstrom) with 57.6% reliability (118/205) for the top 10 ranked conformations and with 74.1% reliability (152/205) for the top 50 ranked conformations of Catalyst-generated conformers, as compared to 22.9% (47/205) and 31.2% (64/205), respectively, in the case of PMI with the same conformer set. | - |
dc.publisher | AMER CHEMICAL SOC | - |
dc.relation.isPartOf | JOURNAL OF CHEMICAL INFORMATION AND MODELING | - |
dc.subject | ORBITAL ELECTRONEGATIVITY METHOD | - |
dc.subject | MODIFIED PARTIAL EQUALIZATION | - |
dc.subject | LAMARCKIAN GENETIC ALGORITHM | - |
dc.subject | FREE-ENERGY DENSITY | - |
dc.subject | AROMATIC-MOLECULES | - |
dc.subject | RECEPTOR DOCKING | - |
dc.subject | FLEXIBLE DOCKING | - |
dc.subject | SOLVATION | - |
dc.subject | BINDING | - |
dc.subject | COMPLEXES | - |
dc.title | Ligand Aligning Method for Molecular Docking: Alignment of Property-Weighted Vectors | - |
dc.type | Article | - |
dc.identifier.doi | 10.1021/ci200501p | - |
dc.type.rims | ART | - |
dc.identifier.bibliographicCitation | JOURNAL OF CHEMICAL INFORMATION AND MODELING, v.52, no.4, pp.984 - 995 | - |
dc.description.journalClass | 1 | - |
dc.identifier.wosid | 000303038000012 | - |
dc.identifier.scopusid | 2-s2.0-84862010592 | - |
dc.citation.endPage | 995 | - |
dc.citation.number | 4 | - |
dc.citation.startPage | 984 | - |
dc.citation.title | JOURNAL OF CHEMICAL INFORMATION AND MODELING | - |
dc.citation.volume | 52 | - |
dc.contributor.affiliatedAuthor | Cho, Kwang-Hwi | - |
dc.type.docType | Article | - |
dc.subject.keywordPlus | ORBITAL ELECTRONEGATIVITY METHOD | - |
dc.subject.keywordPlus | MODIFIED PARTIAL EQUALIZATION | - |
dc.subject.keywordPlus | LAMARCKIAN GENETIC ALGORITHM | - |
dc.subject.keywordPlus | FREE-ENERGY DENSITY | - |
dc.subject.keywordPlus | AROMATIC-MOLECULES | - |
dc.subject.keywordPlus | RECEPTOR DOCKING | - |
dc.subject.keywordPlus | FLEXIBLE DOCKING | - |
dc.subject.keywordPlus | SOLVATION | - |
dc.subject.keywordPlus | BINDING | - |
dc.subject.keywordPlus | COMPLEXES | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
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