DINC: A new AutoDock-based protocol for docking large ligands
Identifieur interne : 000360 ( Main/Exploration ); précédent : 000359; suivant : 000361DINC: A new AutoDock-based protocol for docking large ligands
Auteurs : Ankur Dhanik [États-Unis] ; John S. Mcmurray [États-Unis] ; Lydia E. Kavraki [États-Unis]Source :
- BMC Structural Biology [ 1472-6807 ] ; 2013.
Abstract
Using the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standard docking protocol is less accurate and computationally slow.
In our earlier work, we presented a novel AutoDock-based incremental protocol (DINC) that addresses the limitations of AutoDock's standard protocol by enabling improved docking of large ligands. Instead of docking a large ligand to a target protein in one single step as done in the standard protocol, our protocol docks the large ligand in increments. In this paper, we present three detailed examples of docking using DINC and compare the docking results with those obtained using AutoDock's standard protocol. We summarize the docking results from an extended docking study that was done on 73 protein-ligand complexes comprised of large ligands. We demonstrate not only that DINC is up to 2 orders of magnitude faster than AutoDock's standard protocol, but that it also achieves the speed-up without sacrificing docking accuracy. We also show that positional restraints can be applied to the large ligand using DINC: this is useful when computing a docked conformation of the ligand. Finally, we introduce a webserver for docking large ligands using DINC.
Docking large ligands using DINC is significantly faster than AutoDock's standard protocol without any loss of accuracy. Therefore, DINC could be used as an alternative protocol for docking large ligands. DINC has been implemented as a webserver and is available at
Url:
DOI: 10.1186/1472-6807-13-S1-S11
PubMed: 24564952
PubMed Central: 3952135
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">DINC: A new AutoDock-based protocol for docking large ligands</title><author><name sortKey="Dhanik, Ankur" sort="Dhanik, Ankur" uniqKey="Dhanik A" first="Ankur" last="Dhanik">Ankur Dhanik</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Computer Science, Rice University, Houston, Texas, 77005, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Rice University, Houston, Texas, 77005</wicri:regionArea><wicri:noRegion>77005</wicri:noRegion></affiliation></author><author><name sortKey="Mcmurray, John S" sort="Mcmurray, John S" uniqKey="Mcmurray J" first="John S" last="Mcmurray">John S. Mcmurray</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Experimental Therapeutics, UT MD Anderson Cancer Center, Houston, Texas, 77054, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Experimental Therapeutics, UT MD Anderson Cancer Center, Houston, Texas, 77054</wicri:regionArea><wicri:noRegion>77054</wicri:noRegion></affiliation></author><author><name sortKey="Kavraki, Lydia E" sort="Kavraki, Lydia E" uniqKey="Kavraki L" first="Lydia E" last="Kavraki">Lydia E. Kavraki</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Computer Science, Rice University, Houston, Texas, 77005, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Rice University, Houston, Texas, 77005</wicri:regionArea><wicri:noRegion>77005</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Department of Bioengineering, Rice University, Houston, Texas, 77005, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, Rice University, Houston, Texas, 77005</wicri:regionArea><wicri:noRegion>77005</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24564952</idno><idno type="pmc">3952135</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3952135</idno><idno type="RBID">PMC:3952135</idno><idno type="doi">10.1186/1472-6807-13-S1-S11</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000334</idno><idno type="wicri:Area/Pmc/Curation">000334</idno><idno type="wicri:Area/Pmc/Checkpoint">000339</idno><idno type="wicri:Area/Ncbi/Merge">000502</idno><idno type="wicri:Area/Ncbi/Curation">000502</idno><idno type="wicri:Area/Ncbi/Checkpoint">000502</idno><idno type="wicri:Area/Main/Merge">000361</idno><idno type="wicri:Area/Main/Curation">000360</idno><idno type="wicri:Area/Main/Exploration">000360</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">DINC: A new AutoDock-based protocol for docking large ligands</title><author><name sortKey="Dhanik, Ankur" sort="Dhanik, Ankur" uniqKey="Dhanik A" first="Ankur" last="Dhanik">Ankur Dhanik</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Computer Science, Rice University, Houston, Texas, 77005, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Rice University, Houston, Texas, 77005</wicri:regionArea><wicri:noRegion>77005</wicri:noRegion></affiliation></author><author><name sortKey="Mcmurray, John S" sort="Mcmurray, John S" uniqKey="Mcmurray J" first="John S" last="Mcmurray">John S. Mcmurray</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Experimental Therapeutics, UT MD Anderson Cancer Center, Houston, Texas, 77054, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Experimental Therapeutics, UT MD Anderson Cancer Center, Houston, Texas, 77054</wicri:regionArea><wicri:noRegion>77054</wicri:noRegion></affiliation></author><author><name sortKey="Kavraki, Lydia E" sort="Kavraki, Lydia E" uniqKey="Kavraki L" first="Lydia E" last="Kavraki">Lydia E. Kavraki</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Computer Science, Rice University, Houston, Texas, 77005, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Rice University, Houston, Texas, 77005</wicri:regionArea><wicri:noRegion>77005</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Department of Bioengineering, Rice University, Houston, Texas, 77005, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, Rice University, Houston, Texas, 77005</wicri:regionArea><wicri:noRegion>77005</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Structural Biology</title><idno type="eISSN">1472-6807</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Using the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standard docking protocol is less accurate and computationally slow.</p></sec><sec><title>Results</title><p>In our earlier work, we presented a novel AutoDock-based incremental protocol (DINC) that addresses the limitations of AutoDock's standard protocol by enabling improved docking of large ligands. Instead of docking a large ligand to a target protein in one single step as done in the standard protocol, our protocol docks the large ligand in increments. In this paper, we present three detailed examples of docking using DINC and compare the docking results with those obtained using AutoDock's standard protocol. We summarize the docking results from an extended docking study that was done on 73 protein-ligand complexes comprised of large ligands. We demonstrate not only that DINC is up to 2 orders of magnitude faster than AutoDock's standard protocol, but that it also achieves the speed-up without sacrificing docking accuracy. We also show that positional restraints can be applied to the large ligand using DINC: this is useful when computing a docked conformation of the ligand. Finally, we introduce a webserver for docking large ligands using DINC.</p></sec><sec><title>Conclusions</title><p>Docking large ligands using DINC is significantly faster than AutoDock's standard protocol without any loss of accuracy. Therefore, DINC could be used as an alternative protocol for docking large ligands. DINC has been implemented as a webserver and is available at <ext-link ext-link-type="uri" xlink:href="http://dinc.kavrakilab.org">http://dinc.kavrakilab.org</ext-link>. Applications such as therapeutic drug design, rational vaccine design, and others involving large ligands could benefit from DINC and its webserver implementation.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Finn, P" uniqKey="Finn P">P Finn</name></author><author><name sortKey="Kavraki, Le" uniqKey="Kavraki L">LE Kavraki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Teodoro, Ml" uniqKey="Teodoro M">ML Teodoro</name></author><author><name sortKey="Phillips, Gn" uniqKey="Phillips G">GN Phillips</name></author><author><name sortKey="Kavraki, Le" uniqKey="Kavraki L">LE Kavraki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Anderson, Ac" uniqKey="Anderson A">AC Anderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schneider, G" uniqKey="Schneider G">G 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Bedem</name></author><author><name sortKey="Latombe, Jc" uniqKey="Latombe J">JC Latombe</name></author><author><name sortKey="Halperin Landsberg, I" uniqKey="Halperin Landsberg I">I Halperin-Landsberg</name></author><author><name sortKey="Altman, Rb" uniqKey="Altman R">RB Altman</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Dhanik, Ankur" sort="Dhanik, Ankur" uniqKey="Dhanik A" first="Ankur" last="Dhanik">Ankur Dhanik</name></noRegion><name sortKey="Kavraki, Lydia E" sort="Kavraki, Lydia E" uniqKey="Kavraki L" first="Lydia E" last="Kavraki">Lydia E. Kavraki</name><name sortKey="Kavraki, Lydia E" sort="Kavraki, Lydia E" uniqKey="Kavraki L" first="Lydia E" last="Kavraki">Lydia E. Kavraki</name><name sortKey="Mcmurray, John S" sort="Mcmurray, John S" uniqKey="Mcmurray J" first="John S" last="Mcmurray">John S. Mcmurray</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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