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Article: A gradient-directed Monte Carlo approach for protein design

TitleA gradient-directed Monte Carlo approach for protein design
Authors
Hu, XHu, HBeratan, DNYang, W
KeywordsDiscrete optimization
GDMC
Global optimization
LCAP
Protein sequence design
RosettaDesign
Issue Date2010
PublisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www3.interscience.wiley.com/cgi-bin/jhome/33822
Citation
Journal Of Computational Chemistry, 2010, v. 31 n. 11, p. 2164-2168 How to Cite?
DOI: http://dx.doi.org/10.1002/jcc.21506
AbstractWe develop a new global optimization strategy, gradient-directed Monte Carlo (GDMC) sampling, to optimize protein sequence for a target structure using RosettaDesign. GDMC significantly improves the sampling of sequence space, compared to the classical Monte Carlo search protocol, for a fixed backbone conformation as well as for the simultaneous optimization of sequence and structure. As such, GDMC sampling enhances the efficiency of protein design. © 2010 Wiley Periodicals, Inc.
Persistent Identifierhttp://hdl.handle.net/10722/168466
ISSN
0192-8651
2021 Impact Factor: 3.672
2020 SCImago Journal Rankings: 0.907
ISI Accession Number ID
WOS:000279511200008
References
References in Scopus

 

DC FieldValueLanguage
dc.contributor.authorHu, Xen_US
dc.contributor.authorHu, Hen_US
dc.contributor.authorBeratan, DNen_US
dc.contributor.authorYang, Wen_US
dc.date.accessioned2012-10-08T03:19:18Z-
dc.date.available2012-10-08T03:19:18Z-
dc.date.issued2010en_US
dc.identifier.citationJournal Of Computational Chemistry, 2010, v. 31 n. 11, p. 2164-2168en_US
dc.identifier.issn0192-8651en_US
dc.identifier.urihttp://hdl.handle.net/10722/168466-
dc.description.abstractWe develop a new global optimization strategy, gradient-directed Monte Carlo (GDMC) sampling, to optimize protein sequence for a target structure using RosettaDesign. GDMC significantly improves the sampling of sequence space, compared to the classical Monte Carlo search protocol, for a fixed backbone conformation as well as for the simultaneous optimization of sequence and structure. As such, GDMC sampling enhances the efficiency of protein design. © 2010 Wiley Periodicals, Inc.en_US
dc.languageengen_US
dc.publisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www3.interscience.wiley.com/cgi-bin/jhome/33822en_US
dc.relation.ispartofJournal of Computational Chemistryen_US
dc.subjectDiscrete optimization-
dc.subjectGDMC-
dc.subjectGlobal optimization-
dc.subjectLCAP-
dc.subjectProtein sequence design-
dc.subjectRosettaDesign-
dc.subject.meshAmino Acids - Chemistryen_US
dc.subject.meshComputational Biology - Methodsen_US
dc.subject.meshDrug Designen_US
dc.subject.meshMonte Carlo Methoden_US
dc.subject.meshProtein Conformationen_US
dc.subject.meshProtein Foldingen_US
dc.subject.meshProteins - Chemistryen_US
dc.subject.meshThermodynamicsen_US
dc.titleA gradient-directed Monte Carlo approach for protein designen_US
dc.typeArticleen_US
dc.identifier.emailHu, H:haohu@hku.hken_US
dc.identifier.authorityHu, H=rp00707en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1002/jcc.21506en_US
dc.identifier.pmid20186860-
dc.identifier.scopuseid_2-s2.0-77954251377en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77954251377&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume31en_US
dc.identifier.issue11en_US
dc.identifier.spage2164en_US
dc.identifier.epage2168en_US
dc.identifier.isiWOS:000279511200008-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridHu, X=36646175900en_US
dc.identifier.scopusauthoridHu, H=7404097564en_US
dc.identifier.scopusauthoridBeratan, DN=7006677556en_US
dc.identifier.scopusauthoridYang, W=7407757509en_US
dc.identifier.citeulike7686232-
dc.identifier.issnl0192-8651-

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