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Simple Method for Locating Possible Ligand Binding Sites on Protein Surfaces

Bliznyuk, Andrei; Gready, Jill

Description

A new, fast, and easy-to-implement method, van der Waals-fast Fourier transform (vdW-FFT), for locating possible binding sites on the surface of a protein was developed and tested on a set of 15 different enzyme-ligand complexes. The method scans the whole protein surface and possible ligand orientations in order to find the best geometrical match, which corresponds to the minimum of the modified vdW energy. Two different grids, fine and coarse, and two sets of MM parameters, from the OPLS and...[Show more]

dc.contributor.authorBliznyuk, Andrei
dc.contributor.authorGready, Jill
dc.date.accessioned2015-12-13T23:24:54Z
dc.identifier.issn0192-8651
dc.identifier.urihttp://hdl.handle.net/1885/92438
dc.description.abstractA new, fast, and easy-to-implement method, van der Waals-fast Fourier transform (vdW-FFT), for locating possible binding sites on the surface of a protein was developed and tested on a set of 15 different enzyme-ligand complexes. The method scans the whole protein surface and possible ligand orientations in order to find the best geometrical match, which corresponds to the minimum of the modified vdW energy. Two different grids, fine and coarse, and two sets of MM parameters, from the OPLS and AMBER-94 force fields, were used. The method has been shown to work accurately on the fine grid. On the coarse grid, the vdW-FFT method failed only on two complexes. The C program implementing the method and test set of proteins is available free on our web site: http://biocomp.anu.edu.au/∼aab.
dc.publisherJohn Wiley & Sons Inc
dc.sourceJournal of Computational Chemistry
dc.subjectKeywords: Enzyme active sites; Fast fourier transform (FFT); Molecular docking; Protein binding sites; Van der Waals (vdW) interactions
dc.titleSimple Method for Locating Possible Ligand Binding Sites on Protein Surfaces
dc.typeJournal article
local.description.notesImported from ARIES
local.description.refereedYes
local.identifier.citationvolume20
dc.date.issued1999
local.identifier.absfor060107 - Enzymes
local.identifier.absfor030799 - Theoretical and Computational Chemistry not elsewhere classified
local.identifier.absfor110106 - Medical Biochemistry: Proteins and Peptides (incl. Medical Proteomics)
local.identifier.ariespublicationMigratedxPub23548
local.type.statusPublished Version
local.contributor.affiliationBliznyuk, Andrei, College of Medicine, Biology and Environment, ANU
local.contributor.affiliationGready, Jill, College of Medicine, Biology and Environment, ANU
local.description.embargo2037-12-31
local.bibliographicCitation.issue9
local.bibliographicCitation.startpage983
local.bibliographicCitation.lastpage988
dc.date.updated2015-12-12T09:22:26Z
local.identifier.scopusID2-s2.0-0000416633
CollectionsANU Research Publications

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