Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.
Identifieur interne : 000296 ( PubMed/Corpus ); précédent : 000295; suivant : 000297Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.
Auteurs : Georgios Iakovou ; Steven Hayward ; Stephen D. LaycockSource :
- Journal of molecular graphics & modelling [ 1873-4243 ] ; 2015.
Abstract
Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates.
DOI: 10.1016/j.jmgm.2015.06.003
PubMed: 26186491
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Laycock</name><affiliation><nlm:affiliation>School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom. Electronic address: s.laycock@uea.ac.uk.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26186491</idno><idno type="pmid">26186491</idno><idno type="doi">10.1016/j.jmgm.2015.06.003</idno><idno type="wicri:Area/PubMed/Corpus">000296</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.</title><author><name sortKey="Iakovou, Georgios" sort="Iakovou, Georgios" uniqKey="Iakovou G" first="Georgios" last="Iakovou">Georgios Iakovou</name><affiliation><nlm:affiliation>School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.</nlm:affiliation></affiliation></author><author><name sortKey="Hayward, Steven" sort="Hayward, Steven" uniqKey="Hayward S" first="Steven" last="Hayward">Steven Hayward</name><affiliation><nlm:affiliation>School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom. Electronic address: sjh@cmp.uea.ac.uk.</nlm:affiliation></affiliation></author><author><name sortKey="Laycock, Stephen D" sort="Laycock, Stephen D" uniqKey="Laycock S" first="Stephen D" last="Laycock">Stephen D. Laycock</name><affiliation><nlm:affiliation>School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom. Electronic address: s.laycock@uea.ac.uk.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of molecular graphics & modelling</title><idno type="eISSN">1873-4243</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="In-Process"><PMID Version="1">26186491</PMID><DateCreated><Year>2015</Year><Month>09</Month><Day>14</Day></DateCreated><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-4243</ISSN><JournalIssue CitedMedium="Internet"><Volume>61</Volume><PubDate><Year>2015</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Journal of molecular graphics & modelling</Title><ISOAbbreviation>J. Mol. Graph. Model.</ISOAbbreviation></Journal><ArticleTitle>Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.</ArticleTitle><Pagination><MedlinePgn>1-12</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jmgm.2015.06.003</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S1093-3263(15)30007-3</ELocationID><Abstract><AbstractText>Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates.</AbstractText><CopyrightInformation>Copyright © 2015 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Iakovou</LastName><ForeName>Georgios</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hayward</LastName><ForeName>Steven</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom. Electronic address: sjh@cmp.uea.ac.uk.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Laycock</LastName><ForeName>Stephen D</ForeName><Initials>SD</Initials><AffiliationInfo><Affiliation>School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom. Electronic address: s.laycock@uea.ac.uk.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>06</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Mol Graph Model</MedlineTA><NlmUniqueID>9716237</NlmUniqueID><ISSNLinking>1093-3263</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Force feedback</Keyword><Keyword MajorTopicYN="N">Molecular docking</Keyword><Keyword MajorTopicYN="N">Protein–protein interactions</Keyword><Keyword MajorTopicYN="N">Proximity querying</Keyword><Keyword MajorTopicYN="N">Structure-based drug design</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>4</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>6</Month><Day>8</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>6</Month><Day>9</Day></PubMedPubDate><PubMedPubDate PubStatus="aheadofprint"><Year>2015</Year><Month>6</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>7</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>7</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>7</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26186491</ArticleId><ArticleId IdType="pii">S1093-3263(15)30007-3</ArticleId><ArticleId IdType="doi">10.1016/j.jmgm.2015.06.003</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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