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dc.contributor.authorDhanik, Ankur
Kavraki, Lydia E.
McMurray, John S.
dc.date.accessioned 2017-08-02T22:03:11Z
dc.date.available 2017-08-02T22:03:11Z
dc.date.issued 2012-10-07
dc.identifier.urihttps://hdl.handle.net/1911/96402
dc.description.abstract It is well known that computer-aided docking of large ligands, with many rotatable bonds, is extremely difficult. AutoDock is a widely used docking program that can dock small ligands, with up to 5 or 6 rotatable bonds, accurately and quickly. Docking of larger ligands, however, is not very accurate and is computationally expensive. In this paper we present an AutoDock-based incremental docking protocol which docks a large ligand to its target protein in increments. A fragment of the large ligand is first chosen and then docked. Best docked conformations are incrementally grown and docked again, and this process is repeated until all the atoms of the ligand are docked. Each docking operation is performed using AutoDock. However, in each docking operation only a small number of rotatable bonds are allowed to rotate. We did a systematic docking study on a dataset of 73 protein-ligand complexes derived from the core set of PDBbind database. The number of rotatable bonds in the ligands vary from 7 to 30. Multiple docking experiments were done to evaluate the docking performance of the incremental protocol in comparison to AutoDock’s standard protocol. Results from the study show that, on average over the dataset, docking of large ligands using our incremental protocol is upto 23-fold computationally faster than docking using AutoDock’s standard protocol and also has better or comparable accuracy. We propose that, for docking large ligands, our incremental protocol can be used as an alternative to AutoDock’s standard protocol.
dc.format.extent 26 pp
dc.language.iso eng
dc.rights You are granted permission for the noncommercial reproduction, distribution, display, and performance of this technical report in any format, but this permission is only for a period of forty-five (45) days from the most recent time that you verified that this technical report is still available from the Computer Science Department of Rice University under terms that include this permission. All other rights are reserved by the author(s).
dc.title AutoDock-based incremental docking protocol improves docking of large ligands
dc.type Technical report
dc.date.note October 7, 2012
dc.identifier.digital TR12-03
dc.type.dcmi Text
dc.identifier.citation Dhanik, Ankur, Kavraki, Lydia E. and McMurray, John S.. "AutoDock-based incremental docking protocol improves docking of large ligands." (2012) https://hdl.handle.net/1911/96402.


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