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Article: Analysis of surface structures of hydrogen bonding in protein-ligand interactions using the alpha shape model

TitleAnalysis of surface structures of hydrogen bonding in protein-ligand interactions using the alpha shape model
Authors
Zhou, WYan, HHao, Q
Keywords3d surface
Alpha-shapes
Geometric patterns
Geometric properties
Interface atom
Issue Date2012
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/cplett
Citation
Chemical Physics Letters, 2012, v. 545, p. 125-131 How to Cite?
DOI: http://dx.doi.org/10.1016/j.cplett.2012.07.016
AbstractHydrogen bonding provides useful information for the study of protein-ligand interactions. However, the physical role that a hydrogen bond plays and its 3D surface characteristics in protein-ligand interaction are still not well understood. We apply the 3D alpha shape model to reconstruct the interface of a protein-ligand structure and use solid angles at interface atoms to represent the surface geometric properties of a hydrogen bond. The result shows that 77.2% of the hydrogen bonds show complementary geometric patterns and 95.0% of the protein-ligand complexes contain at least one such hydrogen bond. © 2012 Elsevier B.V. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/164527
ISSN
0009-2614
2023 Impact Factor: 2.8
2023 SCImago Journal Rankings: 0.502
ISI Accession Number ID
WOS:000308199600023

 

DC FieldValueLanguage
dc.contributor.authorZhou, Wen_US
dc.contributor.authorYan, Hen_US
dc.contributor.authorHao, Qen_US
dc.date.accessioned2012-09-20T08:05:19Z-
dc.date.available2012-09-20T08:05:19Z-
dc.date.issued2012en_US
dc.identifier.citationChemical Physics Letters, 2012, v. 545, p. 125-131en_US
dc.identifier.issn0009-2614-
dc.identifier.urihttp://hdl.handle.net/10722/164527-
dc.description.abstractHydrogen bonding provides useful information for the study of protein-ligand interactions. However, the physical role that a hydrogen bond plays and its 3D surface characteristics in protein-ligand interaction are still not well understood. We apply the 3D alpha shape model to reconstruct the interface of a protein-ligand structure and use solid angles at interface atoms to represent the surface geometric properties of a hydrogen bond. The result shows that 77.2% of the hydrogen bonds show complementary geometric patterns and 95.0% of the protein-ligand complexes contain at least one such hydrogen bond. © 2012 Elsevier B.V. All rights reserved.-
dc.languageengen_US
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/cplett-
dc.relation.ispartofChemical Physics Lettersen_US
dc.subject3d surface-
dc.subjectAlpha-shapes-
dc.subjectGeometric patterns-
dc.subjectGeometric properties-
dc.subjectInterface atom-
dc.titleAnalysis of surface structures of hydrogen bonding in protein-ligand interactions using the alpha shape modelen_US
dc.typeArticleen_US
dc.identifier.emailZhou, W: kenandzhou@hotmail.comen_US
dc.identifier.emailHao, Q: qhao@hku.hk-
dc.identifier.authorityHao, Q=rp01332en_US
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.cplett.2012.07.016-
dc.identifier.scopuseid_2-s2.0-84865544265-
dc.identifier.hkuros209312en_US
dc.identifier.volume545en_US
dc.identifier.spage125en_US
dc.identifier.epage131en_US
dc.identifier.isiWOS:000308199600023-
dc.publisher.placeNetherlands-
dc.identifier.citeulike11135584-
dc.identifier.issnl0009-2614-

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