MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening.

BMC Bioinformatics
Nicolas SautonMaria A Miteva

Abstract

The number of protein targets with a known or predicted tri-dimensional structure and of drug-like chemical compounds is growing rapidly and so is the need for new therapeutic compounds or chemical probes. Performing flexible structure-based virtual screening computations on thousands of targets with millions of molecules is intractable to most laboratories nor indeed desirable. Since shape complementarity is of primary importance for most protein-ligand interactions, we have developed a tool/protocol based on rigid-body docking to select compounds that fit well into binding sites. Here we present an efficient multiple conformation rigid-body docking approach, MS-DOCK, which is based on the program DOCK. This approach can be used as the first step of a multi-stage docking/scoring protocol. First, we developed and validated the Multiconf-DOCK tool that generates several conformers per input ligand. Then, each generated conformer (bioactives and 37970 decoys) was docked rigidly using DOCK6 with our optimized protocol into seven different receptor-binding sites. MS-DOCK was able to significantly reduce the size of the initial input library for all seven targets, thereby facilitating subsequent more CPU demanding flexible docking p...Continue Reading

References

Oct 25, 1982·Journal of Molecular Biology·I D KuntzT E Ferrin
Apr 1, 1994·Journal of Computer-aided Molecular Design·M D MillerR P Sheridan
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Apr 5, 2002·Journal of Medicinal Chemistry·Peter L Toogood
Feb 13, 2003·Biopolymers·Mark R McGannFrank K Brown
Jul 3, 2003·Nature Reviews. Drug Discovery·Simon J Teague
Dec 30, 2003·Journal of Medicinal Chemistry·Wely B FlorianoWilliam A Goddard
Jan 23, 2004·Journal of Medicinal Chemistry·Maria KontoyianniGlenn S Sokol
Mar 6, 2004·Journal of Molecular Biology·Claudio N Cavasotto, Ruben A Abagyan
Mar 19, 2004·Journal of Medicinal Chemistry·Richard A FriesnerPeter S Shenkin
Jun 18, 2004·Combinatorial Chemistry & High Throughput Screening·Florence L Stahura, Jürgen Bajorath
Nov 3, 2004·Nature Reviews. Drug Discovery·Douglas B KitchenJürgen Bajorath
Dec 17, 2004·Nature·Brian K Shoichet
Feb 11, 2005·Bioinformatics·Alasdair T R Laurie, Richard M Jackson
Feb 17, 2005·Bioinformatics·Svava Osk JónsdóttirSøren Brunak
Feb 18, 2005·Journal of Medicinal Chemistry·Jean-Christophe MozziconacciLuc Morin-Allory
Apr 6, 2005·Journal of Chemical Information and Modeling·Johannes KirchmairThierry Langer
Jun 10, 2005·Journal of Medicinal Chemistry·Bernd KuhnMartin Stahl
Jun 14, 2005·Journal of Molecular Graphics & Modelling·Yoshifumi FukunishiHaruki Nakamura
Jun 28, 2005·Nucleic Acids Research·C AllandP Tufféry
Aug 17, 2005·Current Topics in Medicinal Chemistry·David M Lorber, Brian K Shoichet
Sep 16, 2005·Journal of Medicinal Chemistry·Maria A MitevaBruno O Villoutreix
Mar 15, 2006·Drug Discovery Today·Werner J GeldenhuysCornelis J Van der Schyf
Apr 4, 2006·Drug Discovery Today·Andrew J W OrryClaudio N Cavasotto
Apr 18, 2006·Current Opinion in Chemical Biology·Chamila N Rupasinghe, Mark R Spaller
Jul 18, 2006·Nucleic Acids Research·Maria A MitevaBruno O Villoutreix
Sep 26, 2006·Drug Discovery Today·Peter J MeekRandy J Zauhar
Sep 29, 2006·Journal of Medicinal Chemistry·Andrew R LeachCatherine E Peishoff
Sep 29, 2006·Journal of Medicinal Chemistry·Julian Tirado-Rives, William L Jorgensen
Sep 29, 2006·Journal of Medicinal Chemistry·Gregory L WarrenMartha S Head
Nov 1, 2006·Current Protein & Peptide Science·Olivier SperandioBruno O Villoutreix
Dec 7, 2006·Journal of Computer-aided Molecular Design·Demetri T MoustakasRobert C Rizzo
Feb 22, 2007·Journal of Medicinal Chemistry·Esther KellenbergerDidier Rognan
Mar 6, 2007·Journal of Molecular Biology·Abdullah KahramanJanet M Thornton
May 9, 2007·Nucleic Acids Research·T Bohme LeiteP Tufféry
May 19, 2007·Current Topics in Medicinal Chemistry·Claudio N Cavasotto, Andrew J W Orry
Jul 25, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kenneth SegersBruno O Villoutreix
Aug 19, 2007·Current Protein & Peptide Science·Bruno O VilloutreixMaria A Miteva
Oct 16, 2007·Current Opinion in Chemical Biology·Campbell McInnes

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Citations

May 12, 2009·Nucleic Acids Research·O SperandioP Tuffery
May 7, 2010·Nucleic Acids Research·Maria A MitevaPierre Tufféry
Oct 18, 2008·BMC Bioinformatics·Tania PenchevaMaria A Miteva
Feb 26, 2014·BMC Structural Biology·Ankur DhanikLydia E Kavraki
Mar 18, 2011·Journal of Cheminformatics·Noel M O'BoyleGeoffrey R Hutchison
Aug 27, 2013·PloS One·Karen R KharJohn Karanicolas
Dec 15, 2010·International Journal of Molecular Sciences·Sheng-You Huang, Xiaoqin Zou
May 7, 2013·Expert Opinion on Drug Discovery·Martiniano BelloJosé Correa-Basurto
Mar 1, 2011·Expert Opinion on Drug Discovery·David LagorceMaria A Miteva
Oct 1, 2010·Expert Opinion on Drug Discovery·Boaz Musafia, Hanoch Senderowitz
Nov 26, 2015·Journal of Chemical Theory and Computation·Li-Li PanKenneth M Merz
Apr 18, 2011·Molecular Informatics·M AtanasovaI Doytchinova
Jul 1, 2012·Molecular Informatics·Gülşah ÇifciE Demet Akten
Sep 1, 2015·Journal of Chemical Information and Modeling·Sheng-You HuangYi Pan
Jun 6, 2015·Archives of Biochemistry and Biophysics·Nuno M F S A CerqueiraMaria J Ramos
Jun 17, 2015·Journal of Chemical Information and Modeling·Indrajit SahaDariusz Plewczynski
Dec 5, 2013·Organic & Biomolecular Chemistry·Cristina RodríguezVicente Gotor
Dec 30, 2014·Trends in Pharmacological Sciences·Yu-Chian Chen
May 28, 2016·Journal of Computational Chemistry·Piero Procacci
Jul 28, 2016·Journal of Chemical Theory and Computation·Musa OzboyaciRebecca C Wade
Feb 17, 2017·Journal of Chemical Information and Modeling·Nils-Ole FriedrichJohannes Kirchmair
Feb 22, 2017·Molecular Informatics·Maria A Miteva, Bruno O Villoutreix
Jul 7, 2017·Journal of Chemical Information and Modeling·Paul C D Hawkins
Nov 8, 2019·Physical Chemistry Chemical Physics : PCCP·Natalia DíazÁngel Martín-Pendás
Sep 12, 2019·Journal of Computer-aided Molecular Design·Woong-Hee Shin, Daisuke Kihara
Feb 20, 2020·Physical Chemistry Chemical Physics : PCCP·Philipp PrachtStefan Grimme
May 17, 2017·Biophysics Reviews·Nataraj S PagadalaJack Tuszynski
Jun 29, 2018·Scientific Reports·Nastaran MeftahiBrian J Smith
Oct 1, 2009·Journal of Chemical Information and Modeling·Axel GriewelMatthias Rarey
Apr 16, 2021·Journal of Molecular Graphics & Modelling·Nastaran MeftahiBrian J Smith

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Methods Mentioned

BETA
in silico methods
NMR
X-ray

Software Mentioned

SBVLS
SPHGEN
FILTER
SiteFinder
Multiconf
FLOG
Openeye
Drugs
Catalyst
DMS

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