Literature DB >> 29606412

Ensemble Docking in Drug Discovery.

Rommie E Amaro1, Jerome Baudry2, John Chodera3, Özlem Demir1, J Andrew McCammon1, Yinglong Miao4, Jeremy C Smith5.   

Abstract

Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that is used in docking candidate ligands. This approach is now well established in the field of early-stage drug discovery. This review gives a historical account of the development of ensemble docking and discusses some pertinent methodological advances in conformational sampling.
Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2018        PMID： 29606412      PMCID： PMC6129458          DOI： 10.1016/j.bpj.2018.02.038

Source DB:  PubMed          Journal:  Biophys J        ISSN： 0006-3495            Impact factor:   4.033


  57 in total

1.  Computing time scales from reaction coordinates by milestoning.

Authors:  Anton K Faradjian; Ron Elber
Journal:  J Chem Phys       Date:  2004-06-15       Impact factor: 3.488

2.  Using generalized ensemble simulations and Markov state models to identify conformational states.

Authors:  Gregory R Bowman; Xuhui Huang; Vijay S Pande
Journal:  Methods       Date:  2009-05-04       Impact factor: 3.608

3.  A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

Authors:  Shweta Purawat; Pek U Ieong; Robert D Malmstrom; Garrett J Chan; Alan K Yeung; Ross C Walker; Ilkay Altintas; Rommie E Amaro
Journal:  Biophys J       Date:  2017-06-20       Impact factor: 4.033

4.  Reviving Antibiotics: Efflux Pump Inhibitors That Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump.

Authors:  Narges Abdali; Jerry M Parks; Keith M Haynes; Julie L Chaney; Adam T Green; David Wolloscheck; John K Walker; Valentin V Rybenkov; Jerome Baudry; Jeremy C Smith; Helen I Zgurskaya
Journal:  ACS Infect Dis       Date:  2016-11-02       Impact factor: 5.084

5.  Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1.

Authors:  Jacob D Durrant; Laurence Hall; Robert V Swift; Melissa Landon; Achim Schnaufer; Rommie E Amaro
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6.  Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models.

Authors:  Nuria Plattner; Frank Noé
Journal:  Nat Commun       Date:  2015-07-02       Impact factor: 14.919

7.  Genome3D: exploiting structure to help users understand their sequences.

Authors:  Tony E Lewis; Ian Sillitoe; Antonina Andreeva; Tom L Blundell; Daniel W A Buchan; Cyrus Chothia; Domenico Cozzetto; José M Dana; Ioannis Filippis; Julian Gough; David T Jones; Lawrence A Kelley; Gerard J Kleywegt; Federico Minneci; Jaina Mistry; Alexey G Murzin; Bernardo Ochoa-Montaño; Matt E Oates; Marco Punta; Owen J L Rackham; Jonathan Stahlhacke; Michael J E Sternberg; Sameer Velankar; Christine Orengo
Journal:  Nucleic Acids Res       Date:  2014-10-27       Impact factor: 16.971

8.  Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations.

Authors:  Fabian Paul; Christoph Wehmeyer; Esam T Abualrous; Hao Wu; Michael D Crabtree; Johannes Schöneberg; Jane Clarke; Christian Freund; Thomas R Weikl; Frank Noé
Journal:  Nat Commun       Date:  2017-10-23       Impact factor: 14.919

9.  Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.

Authors:  Yinglong Miao; Victoria A Feher; J Andrew McCammon
Journal:  J Chem Theory Comput       Date:  2015-07-14       Impact factor: 6.006

10.  Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles.

Authors:  Robert V Swift; Siti A Jusoh; Tavina L Offutt; Eric S Li; Rommie E Amaro
Journal:  J Chem Inf Model       Date:  2016-05-03       Impact factor: 4.956
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  103 in total

1.  Discovery and Characterization of the Biflavones From Ginkgo biloba as Highly Specific and Potent Inhibitors Against Human Carboxylesterase 2.

Authors:  Yun-Qing Song; Rong-Jing He; Dan Pu; Xiao-Qing Guan; Jin-Hui Shi; Yao-Guang Li; Jie Hou; Shou-Ning Jia; Wei-Wei Qin; Sheng-Quan Fang; Guang-Bo Ge
Journal:  Front Pharmacol       Date:  2021-05-18       Impact factor: 5.810

2.  Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria.

Authors:  Yu-Ming M Huang; Jason Munguia; Yinglong Miao; Victor Nizet; J Andrew McCammon
Journal:  Chem Biol Drug Des       Date:  2019-02-19       Impact factor: 2.817

3.  Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking.

Authors:  Helen M Deeks; Rebecca K Walters; Stephanie R Hare; Michael B O'Connor; Adrian J Mulholland; David R Glowacki
Journal:  PLoS One       Date:  2020-03-11       Impact factor: 3.240

4.  Structural basis for ligand modulation of the CCR2 conformational landscape.

Authors:  Bryn C Taylor; Christopher T Lee; Rommie E Amaro
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-11       Impact factor: 11.205

5.  Design and development of FGF-23 antagonists: Definition of the pharmacophore and initial structure-activity relationships probed by synthetic analogues.

Authors:  Ryan P Downs; Zhousheng Xiao; Munachi O Ikedionwu; Jacob W Cleveland; Ai Lin Chin; Abigail E Cafferty; L Darryl Quarles; Jesse D Carrick
Journal:  Bioorg Med Chem       Date:  2020-11-18       Impact factor: 3.641

6.  Ligand binding free-energy calculations with funnel metadynamics.

Authors:  Stefano Raniolo; Vittorio Limongelli
Journal:  Nat Protoc       Date:  2020-08-19       Impact factor: 13.491

7.  Assessing and improving the performance of consensus docking strategies using the DockBox package.

Authors:  Jordane Preto; Francesco Gentile
Journal:  J Comput Aided Mol Des       Date:  2019-10-01       Impact factor: 3.686

Review 8.  Investigating Cryptic Binding Sites by Molecular Dynamics Simulations.

Authors:  Antonija Kuzmanic; Gregory R Bowman; Jordi Juarez-Jimenez; Julien Michel; Francesco L Gervasio
Journal:  Acc Chem Res       Date:  2020-03-05       Impact factor: 22.384

Review 9.  Computational Dissection of Membrane Transport at a Microscopic Level.

Authors:  Tao Jiang; Po-Chao Wen; Noah Trebesch; Zhiyu Zhao; Shashank Pant; Karan Kapoor; Mrinal Shekhar; Emad Tajkhorshid
Journal:  Trends Biochem Sci       Date:  2019-12-05       Impact factor: 13.807

10.  D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings.

Authors:  Zied Gaieb; Conor D Parks; Michael Chiu; Huanwang Yang; Chenghua Shao; W Patrick Walters; Millard H Lambert; Neysa Nevins; Scott D Bembenek; Michael K Ameriks; Tara Mirzadegan; Stephen K Burley; Rommie E Amaro; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2019-01-10       Impact factor: 3.686
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