The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.
Identifieur interne : 001188 ( Main/Exploration ); précédent : 001187; suivant : 001189The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.
Auteurs : P. Luginbühl [Suisse] ; P. Güntert ; M. Billeter ; K. WüthrichSource :
- Journal of biomolecular NMR [ 0925-2738 ] ; 1996.
Descripteurs français
- KwdFr :
- MESH :
- composition chimique : Eau, Protéines, Protéines de protozoaire.
- Glutarédoxines, Logiciel, Modèles moléculaires, Modèles théoriques, Mouvement, Oxidoreductases, Simulation numérique.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins, Protozoan Proteins, Water.
- chemical : Glutaredoxins, Oxidoreductases.
- Computer Simulation, Models, Molecular, Models, Theoretical, Movement, Software.
Abstract
A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.
DOI: 10.1007/BF00211160
PubMed: 8914272
Affiliations:
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Güntert</name></author><author><name sortKey="Billeter, M" sort="Billeter, M" uniqKey="Billeter M" first="M" last="Billeter">M. Billeter</name></author><author><name sortKey="Wuthrich, K" sort="Wuthrich, K" uniqKey="Wuthrich K" first="K" last="Wüthrich">K. Wüthrich</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1996">1996</date><idno type="RBID">pubmed:8914272</idno><idno type="pmid">8914272</idno><idno type="doi">10.1007/BF00211160</idno><idno type="wicri:Area/Main/Corpus">001192</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001192</idno><idno type="wicri:Area/Main/Curation">001192</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">001192</idno><idno type="wicri:Area/Main/Exploration">001192</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.</title><author><name sortKey="Luginbuhl, P" sort="Luginbuhl, P" uniqKey="Luginbuhl P" first="P" last="Luginbühl">P. Luginbühl</name><affiliation wicri:level="3"><nlm:affiliation>Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich</wicri:regionArea><placeName><settlement type="city">Zurich</settlement><region nuts="3" type="region">Canton de Zurich</region></placeName></affiliation></author><author><name sortKey="Guntert, P" sort="Guntert, P" uniqKey="Guntert P" first="P" last="Güntert">P. Güntert</name></author><author><name sortKey="Billeter, M" sort="Billeter, M" uniqKey="Billeter M" first="M" last="Billeter">M. Billeter</name></author><author><name sortKey="Wuthrich, K" sort="Wuthrich, K" uniqKey="Wuthrich K" first="K" last="Wüthrich">K. Wüthrich</name></author></analytic><series><title level="j">Journal of biomolecular NMR</title><idno type="ISSN">0925-2738</idno><imprint><date when="1996" type="published">1996</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computer Simulation (MeSH)</term><term>Glutaredoxins (MeSH)</term><term>Models, Molecular (MeSH)</term><term>Models, Theoretical (MeSH)</term><term>Movement (MeSH)</term><term>Oxidoreductases (MeSH)</term><term>Proteins (chemistry)</term><term>Protozoan Proteins (chemistry)</term><term>Software (MeSH)</term><term>Water (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Eau (composition chimique)</term><term>Glutarédoxines (MeSH)</term><term>Logiciel (MeSH)</term><term>Modèles moléculaires (MeSH)</term><term>Modèles théoriques (MeSH)</term><term>Mouvement (MeSH)</term><term>Oxidoreductases (MeSH)</term><term>Protéines (composition chimique)</term><term>Protéines de protozoaire (composition chimique)</term><term>Simulation numérique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term><term>Protozoan Proteins</term><term>Water</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Glutaredoxins</term><term>Oxidoreductases</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Eau</term><term>Protéines</term><term>Protéines de protozoaire</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Models, Molecular</term><term>Models, Theoretical</term><term>Movement</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Glutarédoxines</term><term>Logiciel</term><term>Modèles moléculaires</term><term>Modèles théoriques</term><term>Mouvement</term><term>Oxidoreductases</term><term>Simulation numérique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">8914272</PMID><DateCompleted><Year>1996</Year><Month>12</Month><Day>17</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>20</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0925-2738</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><Issue>2</Issue><PubDate><Year>1996</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Journal of biomolecular NMR</Title><ISOAbbreviation>J Biomol NMR</ISOAbbreviation></Journal><ArticleTitle>The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.</ArticleTitle><Pagination><MedlinePgn>136-46</MedlinePgn></Pagination><Abstract><AbstractText>A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with different force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Luginbühl</LastName><ForeName>P</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Güntert</LastName><ForeName>P</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Billeter</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Wüthrich</LastName><ForeName>K</ForeName><Initials>K</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Biomol NMR</MedlineTA><NlmUniqueID>9110829</NlmUniqueID><ISSNLinking>0925-2738</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D054477">Glutaredoxins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011506">Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015800">Protozoan Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C081617">mating pheromone 2, Euplotes raikovi</NameOfSubstance></Chemical><Chemical><RegistryNumber>059QF0KO0R</RegistryNumber><NameOfSubstance UI="D014867">Water</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.-</RegistryNumber><NameOfSubstance UI="D010088">Oxidoreductases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>J Biomol NMR 1997 Feb;9(2):212</RefSource></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="Y">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054477" MajorTopicYN="N">Glutaredoxins</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="Y">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008962" MajorTopicYN="N">Models, Theoretical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009068" MajorTopicYN="N">Movement</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010088" MajorTopicYN="Y">Oxidoreductases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011506" MajorTopicYN="N">Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015800" MajorTopicYN="N">Protozoan Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014867" MajorTopicYN="N">Water</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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Billeter</name><name sortKey="Guntert, P" sort="Guntert, P" uniqKey="Guntert P" first="P" last="Güntert">P. Güntert</name><name sortKey="Wuthrich, K" sort="Wuthrich, K" uniqKey="Wuthrich K" first="K" last="Wüthrich">K. Wüthrich</name></noCountry><country name="Suisse"><region name="Canton de Zurich"><name sortKey="Luginbuhl, P" sort="Luginbuhl, P" uniqKey="Luginbuhl P" first="P" last="Luginbühl">P. Luginbühl</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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