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dc.contributor.authorDhanik, Ankur
McMurray, John S.
Kavraki, Lydia E.
dc.date.accessioned 2016-03-24T18:24:34Z
dc.date.available 2016-03-24T18:24:34Z
dc.date.issued 2013
dc.identifier.citation Dhanik, Ankur, McMurray, John S. and Kavraki, Lydia E.. "DINC: A new AutoDock-based protocol for docking large ligands." BMC Structural Biology, 13(Suppl 1), (2013) BioMed Central: http://dx.doi.org/10.1186/1472-6807-13-S1-S11.
dc.identifier.urihttps://hdl.handle.net/1911/88639
dc.description.abstractBackground: 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. Results: 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. Conclusions: 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 http://?dinc.?kavrakilab.?org. Applications such as therapeutic drug design, rational vaccine design, and others involving large ligands could benefit from DINC and its webserver implementation.
dc.language.iso eng
dc.publisher BioMed Central
dc.rightsThis article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/licenses/by/2.0/
dc.title DINC: A new AutoDock-based protocol for docking large ligands
dc.type Journal article
dc.contributor.funder Cancer Prevention Institute of Texas
dc.contributor.funder Texas Higher Education Coordinating Board
dc.contributor.funder National Science Foundation
dc.contributor.funder National Cancer Institute
dc.contributor.funder John and Ann Doerr Fund for Computational Biomedicine at Rice University
dc.citation.journalTitle BMC Structural Biology
dc.citation.volumeNumber 13(Suppl 1)
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1186/1472-6807-13-S1-S11
dc.identifier.pmcid PMC3952135
dc.identifier.pmid 24564952
dc.identifier.grantID RP101489 (Cancer Prevention Institute of Texas)
dc.identifier.grantID NHARP 01907 (Texas Higher Education Coordinating Board)
dc.identifier.grantID ABI-0960612 (National Science Foundation)
dc.identifier.grantID RO1 CA096652 (National Cancer Institute)
dc.identifier.grantID OCI-0959097 (National Science Foundation)
dc.type.publication publisher version


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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated.