Blind docking of 260 protein-ligand complexes with EADock 2.0

Journal of Computational Chemistry
Aurélien GrosdidierOlivier Michielin

Abstract

Molecular docking softwares are one of the important tools of modern drug development pipelines. The promising achievements of the last 10 years emphasize the need for further improvement, as reflected by several recent publications (Leach et al., J Med Chem 2006, 49, 5851; Warren et al., J Med Chem 2006, 49, 5912). Our initial approach, EADock, showed a good performance in reproducing the experimental binding modes for a set of 37 different ligand-protein complexes (Grosdidier et al., Proteins 2007, 67, 1010). This article presents recent improvements regarding the scoring and sampling aspects over the initial implementation, as well as a new seeding procedure based on the detection of cavities, opening the door to blind docking with EADock. These enhancements were validated on 260 complexes taken from the high quality Ligand Protein Database [LPDB, (Roche et al., J Med Chem 2001, 44, 3592)]. Two issues were identified: first, the quality of the initial structures cannot be assumed and a manual inspection and/or a search in the literature are likely to be required to achieve the best performance. Second the description of interactions involving metal ions still has to be improved. Nonetheless, a remarkable success rate of 65% ...Continue Reading

References

Aug 15, 1998·Journal of Molecular Graphics & Modelling·M HendlichG Barnickel
Oct 19, 2001·Journal of Medicinal Chemistry·O RocheC L Brooks
Jun 19, 2002·Protein Science : a Publication of the Protein Society·Csaba Hetényi, David van der Spoel
May 28, 2004·Journal of Medicinal Chemistry·Philippe FerraraCharles L Brooks
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Nov 5, 2004·Journal of Computational Chemistry·Maria KontoyianniLaura M McClellan
Mar 11, 2005·Molecular & Cellular Proteomics : MCP·Jianghong AnRuben Abagyan
Jun 7, 2005·Proteins·Jason C ColeRobin Taylor
Nov 24, 2005·Proteins·Fabian GlaserJanet M Thornton
Feb 8, 2006·FEBS Letters·Csaba Hetényi, David van der Spoel
Jul 25, 2006·Proteins·Sérgio Filipe SousaMaria João Ramos
Sep 29, 2006·Journal of Medicinal Chemistry·Andrew R LeachCatherine E Peishoff
Sep 29, 2006·Journal of Medicinal Chemistry·Gregory L WarrenMartha S Head
Jan 4, 2007·Nature Reviews. Drug Discovery·Simon Frantz
Feb 3, 2007·Journal of Computational Chemistry·Ruth HueyDavid S Goodsell
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

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Citations

Oct 8, 2013·Bioorganic & Medicinal Chemistry Letters·Alessandra MonacoYann Seimbille
May 24, 2012·Journal of Medicinal Chemistry·Ute F RöhrigOlivier Michielin
Mar 24, 2012·Proceedings of the National Academy of Sciences of the United States of America·Pär SöderhjelmMichele Parrinello
Jun 1, 2011·Nucleic Acids Research·Aurélien GrosdidierOlivier Michielin
Jun 25, 2010·The Journal of Chemical Physics·O Anatole von Lilienfeld, Alexandre Tkatchenko
Jul 19, 2014·European Journal of Medicinal Chemistry·Ute F RöhrigOlivier Michielin
May 7, 2013·Expert Opinion on Drug Discovery·Martiniano BelloJosé Correa-Basurto
Mar 18, 2011·Protein Science : a Publication of the Protein Society·Csaba Hetényi, David van der Spoel
Mar 2, 2011·Journal of Molecular Recognition : JMR·Elizabeth YurievPaul A Ramsland
Sep 17, 2013·Lung Cancer : Journal of the International Association for the Study of Lung Cancer·Oliver GautschiJoachim Diebold
Feb 6, 2013·Lung Cancer : Journal of the International Association for the Study of Lung Cancer·Nadine DemierreSolange Peters
Dec 3, 2015·PLoS Computational Biology·Pradeep Anand RavindranathMichel F Sanner
May 5, 2011·Journal of Computational Chemistry·Vincent ZoeteOlivier Michielin
Jan 27, 2010·Journal of Molecular Recognition : JMR·Vincent ZoeteOlivier Michielin
Jul 3, 2019·Acta Pharmacologica Sinica·Yang LiuYang Cao
Sep 22, 2019·International Journal of Molecular Sciences·Antoine Daina, Vincent Zoete
Oct 17, 2019·Marine Drugs·Luca AmbrosinoMaria Luisa Chiusano
Nov 13, 2015·Journal of Computational Chemistry·Vincent ZoeteOlivier Michielin
May 5, 2011·Journal of Computational Chemistry·Aurélien GrosdidierOlivier Michielin
Jan 9, 2010·Journal of Medicinal Chemistry·Ute F RöhrigOlivier Michielin
Oct 10, 2014·Journal of Chemical Information and Modeling·Prasad ChaskarUte F Röhrig
Oct 14, 2021·Journal of Biomolecular Structure & Dynamics·Gianvito GrassoMarco A Deriu
Nov 7, 2021·Journal of Computational Chemistry·Sai L VankayalaH Lee Woodcock

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