HapticV1, PubMed, Corpus, bibRecord, 001199

Interacting with the biomolecular solvent accessible surface via a haptic feedback device.

Identifieur interne : 001199 ( PubMed/Corpus ); précédent : 001198; suivant : 001200

Interacting with the biomolecular solvent accessible surface via a haptic feedback device.

Auteurs : Matthew B. Stocks ; Steven Hayward ; Stephen D. Laycock

Source :

BMC structural biology [ 1472-6807 ] ; 2009.

RBID : pubmed:19860901

English descriptors

KwdEn :
- Acetylcholinesterase (chemistry), Alcohol Dehydrogenase (chemistry), Algorithms, Catalytic Domain, Computer Graphics, Computer Simulation, Feedback, Imaging, Three-Dimensional, Software, Solvents (chemistry).
MESH :
- chemical , chemistry : Acetylcholinesterase, Alcohol Dehydrogenase, Solvents.
- Algorithms, Catalytic Domain, Computer Graphics, Computer Simulation, Feedback, Imaging, Three-Dimensional, Software.

Abstract

From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation.

DOI: 10.1186/1472-6807-9-69
PubMed: 19860901

Links to Exploration step

pubmed:19860901

Le document en format XML

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<author><name sortKey="Stocks, Matthew B" sort="Stocks, Matthew B" uniqKey="Stocks M" first="Matthew B" last="Stocks">Matthew B. Stocks</name>
<affiliation><nlm:affiliation>School of Computing Sciences, University of East Anglia, Norwich, UK. matthew.stocks@uea.ac.uk</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Hayward, Steven" sort="Hayward, Steven" uniqKey="Hayward S" first="Steven" last="Hayward">Steven Hayward</name>
</author>
<author><name sortKey="Laycock, Stephen D" sort="Laycock, Stephen D" uniqKey="Laycock S" first="Stephen D" last="Laycock">Stephen D. Laycock</name>
</author>
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<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2009">2009</date>
<idno type="doi">10.1186/1472-6807-9-69</idno>
<idno type="RBID">pubmed:19860901</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Interacting with the biomolecular solvent accessible surface via a haptic feedback device.</title>
<author><name sortKey="Stocks, Matthew B" sort="Stocks, Matthew B" uniqKey="Stocks M" first="Matthew B" last="Stocks">Matthew B. Stocks</name>
<affiliation><nlm:affiliation>School of Computing Sciences, University of East Anglia, Norwich, UK. matthew.stocks@uea.ac.uk</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Hayward, Steven" sort="Hayward, Steven" uniqKey="Hayward S" first="Steven" last="Hayward">Steven Hayward</name>
</author>
<author><name sortKey="Laycock, Stephen D" sort="Laycock, Stephen D" uniqKey="Laycock S" first="Stephen D" last="Laycock">Stephen D. Laycock</name>
</author>
</analytic>
<series><title level="j">BMC structural biology</title>
<idno type="eISSN">1472-6807</idno>
<imprint><date when="2009" type="published">2009</date>
</imprint>
</series>
</biblStruct>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Acetylcholinesterase (chemistry)</term>
<term>Alcohol Dehydrogenase (chemistry)</term>
<term>Algorithms</term>
<term>Catalytic Domain</term>
<term>Computer Graphics</term>
<term>Computer Simulation</term>
<term>Feedback</term>
<term>Imaging, Three-Dimensional</term>
<term>Software</term>
<term>Solvents (chemistry)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Acetylcholinesterase</term>
<term>Alcohol Dehydrogenase</term>
<term>Solvents</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Catalytic Domain</term>
<term>Computer Graphics</term>
<term>Computer Simulation</term>
<term>Feedback</term>
<term>Imaging, Three-Dimensional</term>
<term>Software</term>
</keywords>
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<front><div type="abstract" xml:lang="en">From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation.</div>
</front>
</TEI>
<pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">19860901</PMID>
<DateCreated><Year>2009</Year>
<Month>11</Month>
<Day>10</Day>
</DateCreated>
<DateCompleted><Year>2010</Year>
<Month>01</Month>
<Day>22</Day>
</DateCompleted>
<DateRevised><Year>2014</Year>
<Month>12</Month>
<Day>07</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1472-6807</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>9</Volume>
<PubDate><Year>2009</Year>
</PubDate>
</JournalIssue>
<Title>BMC structural biology</Title>
<ISOAbbreviation>BMC Struct. Biol.</ISOAbbreviation>
</Journal>
<ArticleTitle>Interacting with the biomolecular solvent accessible surface via a haptic feedback device.</ArticleTitle>
<Pagination><MedlinePgn>69</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/1472-6807-9-69</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations.</AbstractText>
<AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">By using the software, named HaptiMol ISAS (available from http://www.haptimol.co.uk), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Stocks</LastName>
<ForeName>Matthew B</ForeName>
<Initials>MB</Initials>
<AffiliationInfo><Affiliation>School of Computing Sciences, University of East Anglia, Norwich, UK. matthew.stocks@uea.ac.uk</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hayward</LastName>
<ForeName>Steven</ForeName>
<Initials>S</Initials>
</Author>
<Author ValidYN="Y"><LastName>Laycock</LastName>
<ForeName>Stephen D</ForeName>
<Initials>SD</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2009</Year>
<Month>10</Month>
<Day>27</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>BMC Struct Biol</MedlineTA>
<NlmUniqueID>101088689</NlmUniqueID>
<ISSNLinking>1472-6807</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D012997">Solvents</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>EC 1.1.1.1</RegistryNumber>
<NameOfSubstance UI="D000426">Alcohol Dehydrogenase</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>EC 3.1.1.7</RegistryNumber>
<NameOfSubstance UI="D000110">Acetylcholinesterase</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2002 Jan;18(1):140-6</RefSource>
<PMID Version="1">11836222</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>J Mol Biol. 1978 Mar 15;119(4):537-55</RefSource>
<PMID Version="1">642001</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Biophys J. 2006 Sep 1;91(5):1823-31</RefSource>
<PMID Version="1">16714351</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Biochemistry. 1994 Jan 11;33(1):23-32</RefSource>
<PMID Version="1">8286346</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Science. 1983 Aug 19;221(4612):709-13</RefSource>
<PMID Version="1">6879170</PMID>
</CommentsCorrections>
</CommentsCorrectionsList>
<MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D000110">Acetylcholinesterase</DescriptorName>
<QualifierName MajorTopicYN="N" UI="Q000737">chemistry</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="N" UI="D000426">Alcohol Dehydrogenase</DescriptorName>
<QualifierName MajorTopicYN="N" UI="Q000737">chemistry</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="N" UI="D000465">Algorithms</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="N" UI="D020134">Catalytic Domain</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="N" UI="D003196">Computer Graphics</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="N" UI="D003198">Computer Simulation</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="N" UI="D005246">Feedback</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="N" UI="D021621">Imaging, Three-Dimensional</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="Y" UI="D012984">Software</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="N" UI="D012997">Solvents</DescriptorName>
<QualifierName MajorTopicYN="Y" UI="Q000737">chemistry</QualifierName>
</MeshHeading>
</MeshHeadingList>
<OtherID Source="NLM">PMC2774689</OtherID>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2009</Year>
<Month>8</Month>
<Day>3</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2009</Year>
<Month>10</Month>
<Day>27</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="aheadofprint"><Year>2009</Year>
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<PubMedPubDate PubStatus="medline"><Year>2010</Year>
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</History>
<PublicationStatus>epublish</PublicationStatus>
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Interacting with the biomolecular solvent accessible surface via a haptic feedback device.

Interacting with the biomolecular solvent accessible surface via a haptic feedback device.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki