Applying forces to elastic network models of large biomolecules using a haptic feedback device.
Identifieur interne : 000F66 ( PubMed/Corpus ); précédent : 000F65; suivant : 000F67Applying forces to elastic network models of large biomolecules using a haptic feedback device.
Auteurs : M B Stocks ; S D Laycock ; S. HaywardSource :
- Journal of computer-aided molecular design [ 1573-4951 ] ; 2011.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins.
- Animals, Databases, Protein, Elasticity, Humans, Molecular Dynamics Simulation, Software, User-Computer Interface.
Abstract
Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version.
DOI: 10.1007/s10822-010-9410-0
PubMed: 21240622
Links to Exploration step
pubmed:21240622Le document en format XML
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Hayward</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="doi">10.1007/s10822-010-9410-0</idno><idno type="RBID">pubmed:21240622</idno><idno type="pmid">21240622</idno><idno type="wicri:Area/PubMed/Corpus">000F66</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Applying forces to elastic network models of large biomolecules using a haptic feedback device.</title><author><name sortKey="Stocks, M B" sort="Stocks, M B" uniqKey="Stocks M" first="M B" last="Stocks">M B Stocks</name><affiliation><nlm:affiliation>School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Laycock, S D" sort="Laycock, S D" uniqKey="Laycock S" first="S D" last="Laycock">S D Laycock</name></author><author><name sortKey="Hayward, S" sort="Hayward, S" uniqKey="Hayward S" first="S" last="Hayward">S. Hayward</name></author></analytic><series><title level="j">Journal of computer-aided molecular design</title><idno type="eISSN">1573-4951</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Databases, Protein</term><term>Elasticity</term><term>Humans</term><term>Molecular Dynamics Simulation</term><term>Proteins (chemistry)</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Databases, Protein</term><term>Elasticity</term><term>Humans</term><term>Molecular Dynamics Simulation</term><term>Software</term><term>User-Computer Interface</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">21240622</PMID><DateCreated><Year>2011</Year><Month>03</Month><Day>09</Day></DateCreated><DateCompleted><Year>2011</Year><Month>06</Month><Day>14</Day></DateCompleted><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1573-4951</ISSN><JournalIssue CitedMedium="Internet"><Volume>25</Volume><Issue>3</Issue><PubDate><Year>2011</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Journal of computer-aided molecular design</Title><ISOAbbreviation>J. Comput. Aided Mol. Des.</ISOAbbreviation></Journal><ArticleTitle>Applying forces to elastic network models of large biomolecules using a haptic feedback device.</ArticleTitle><Pagination><MedlinePgn>203-11</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s10822-010-9410-0</ELocationID><Abstract><AbstractText>Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Stocks</LastName><ForeName>M B</ForeName><Initials>MB</Initials><AffiliationInfo><Affiliation>School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Laycock</LastName><ForeName>S D</ForeName><Initials>SD</Initials></Author><Author ValidYN="Y"><LastName>Hayward</LastName><ForeName>S</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>01</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Comput Aided Mol Des</MedlineTA><NlmUniqueID>8710425</NlmUniqueID><ISSNLinking>0920-654X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011506">Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D000818">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D030562">Databases, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D004548">Elasticity</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D006801">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="Y" UI="D056004">Molecular Dynamics Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D011506">Proteins</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000737">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="Y" UI="D012984">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D014584">User-Computer Interface</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2010</Year><Month>9</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2010</Year><Month>12</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="aheadofprint"><Year>2011</Year><Month>1</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>1</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>1</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2011</Year><Month>6</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="doi">10.1007/s10822-010-9410-0</ArticleId><ArticleId IdType="pubmed">21240622</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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