Literature DB >> 26103917

Covalent docking using autodock: Two-point attractor and flexible side chain methods.

Giulia Bianco1, Stefano Forli2, David S Goodsell2, Arthur J Olson2.   

Abstract

We describe two methods of automated covalent docking using Autodock4: the two-point attractor method and the flexible side chain method. Both methods were applied to a training set of 20 diverse protein-ligand covalent complexes, evaluating their reliability in predicting the crystallographic pose of the ligands. The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested. Both methods are freely available at the AutoDock website (http://autodock.scripps.edu).
© 2015 The Protein Society.

Keywords:  computational docking; computer-aided drug design; covalent inhibitors; ligand-protein interactions

Mesh：

Substances：

Year:  2015        PMID： 26103917      PMCID： PMC4815316          DOI： 10.1002/pro.2733

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  20 in total

1.  Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking.

Authors:  B Kramer; M Rarey; T Lengauer
Journal:  Proteins       Date:  1999-11-01

2.  Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock.

Authors:  Fredrik Osterberg; Garrett M Morris; Michel F Sanner; Arthur J Olson; David S Goodsell
Journal:  Proteins       Date:  2002-01-01

3.  Improved protein-ligand docking using GOLD.

Authors:  Marcel L Verdonk; Jason C Cole; Michael J Hartshorn; Christopher W Murray; Richard D Taylor
Journal:  Proteins       Date:  2003-09-01

Review 4.  Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

Authors:  N Moitessier; P Englebienne; D Lee; J Lawandi; C R Corbeil
Journal:  Br J Pharmacol       Date:  2007-11-26       Impact factor: 8.739

5.  Lennard-Jones potential and dummy atom settings to overcome the AUTODOCK limitation in treating flexible ring systems.

Authors:  Stefano Forli; Maurizio Botta
Journal:  J Chem Inf Model       Date:  2007-06-22       Impact factor: 4.956

6.  Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin".

Authors:  Nicholas R Silvaggi; Helen R Josephine; Alexandre P Kuzin; Rajesh Nagarajan; R F Pratt; Judith A Kelly
Journal:  J Mol Biol       Date:  2005-01-21       Impact factor: 5.469

7.  The design and enzyme-bound crystal structure of indoline based peptidomimetic inhibitors of hepatitis C virus NS3 protease.

Authors:  Jesus M Ontoria; Stefania Di Marco; Immacolata Conte; M Emilia Di Francesco; Cristina Gardelli; Uwe Koch; Victor G Matassa; Marco Poma; Christian Steinkühler; Cinzia Volpari; Steven Harper
Journal:  J Med Chem       Date:  2004-12-16       Impact factor: 7.446

8.  SAR and mode of action of novel non-nucleoside inhibitors of hepatitis C NS5b RNA polymerase.

Authors:  Jay P Powers; Derek E Piper; Yang Li; Veronica Mayorga; John Anzola; James M Chen; Juan C Jaen; Gary Lee; Jinqian Liu; M Greg Peterson; George R Tonn; Qiuping Ye; Nigel P C Walker; Zhulun Wang
Journal:  J Med Chem       Date:  2006-02-09       Impact factor: 7.446

9.  Covalent docking of large libraries for the discovery of chemical probes.

Authors:  Nir London; Rand M Miller; Shyam Krishnan; Kenji Uchida; John J Irwin; Oliv Eidam; Lucie Gibold; Peter Cimermančič; Richard Bonnet; Brian K Shoichet; Jack Taunton
Journal:  Nat Chem Biol       Date:  2014-10-26       Impact factor: 15.040

10.  AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.

Authors:  Diogo Santos-Martins; Stefano Forli; Maria João Ramos; Arthur J Olson
Journal:  J Chem Inf Model       Date:  2014-07-18       Impact factor: 4.956
View more
  40 in total

Review 1.  Docking Screens for Novel Ligands Conferring New Biology.

Authors:  John J Irwin; Brian K Shoichet
Journal:  J Med Chem       Date:  2016-03-15       Impact factor: 7.446

2.  Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12.

Authors:  Jamison P Huddleston; James B Thoden; Brandon J Dopkins; Tamari Narindoshvili; Blair J Fose; Hazel M Holden; Frank M Raushel
Journal:  Biochemistry       Date:  2019-07-26       Impact factor: 3.162

3.  L-DOPA-quinone Mediated Recovery from GIRK Channel Firing Inhibition in Dopaminergic Neurons.

Authors:  Bruno M Bizzarri; Lorenzo Botta; Daniela Aversa; Nicola B Mercuri; Giulio Poli; Alessandro Barbieri; Nicola Berretta; Raffaele Saladino
Journal:  ACS Med Chem Lett       Date:  2019-01-09       Impact factor: 4.345

4.  Biased Docking for Protein-Ligand Pose Prediction.

Authors:  Juan Pablo Arcon; Adrián G Turjanski; Marcelo A Martí; Stefano Forli
Journal:  Methods Mol Biol       Date:  2021

5.  Targeting the Unique Mechanism of Bacterial 1-Deoxy-d-xylulose-5-phosphate Synthase.

Authors:  David Bartee; Caren L Freel Meyers
Journal:  Biochemistry       Date:  2018-07-06       Impact factor: 3.162

6.  Structural Analysis of Cj1427, an Essential NAD-Dependent Dehydrogenase for the Biosynthesis of the Heptose Residues in the Capsular Polysaccharides of Campylobacter jejuni.

Authors:  Jamison P Huddleston; Thomas K Anderson; Keelan D Spencer; James B Thoden; Frank M Raushel; Hazel M Holden
Journal:  Biochemistry       Date:  2020-03-23       Impact factor: 3.162

Review 7.  Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors.

Authors:  Giulia Bianco; David S Goodsell; Stefano Forli
Journal:  Trends Pharmacol Sci       Date:  2020-11-02       Impact factor: 14.819

8.  Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.

Authors:  Xiaobo Wan; Tangpo Yang; Adolfo Cuesta; Xiaming Pang; Trent E Balius; John J Irwin; Brian K Shoichet; Jack Taunton
Journal:  J Am Chem Soc       Date:  2020-03-04       Impact factor: 15.419

9.  An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells.

Authors:  Ekaterina V Vinogradova; Xiaoyu Zhang; David Remillard; Daniel C Lazar; Radu M Suciu; Yujia Wang; Giulia Bianco; Yu Yamashita; Vincent M Crowley; Michael A Schafroth; Minoru Yokoyama; David B Konrad; Kenneth M Lum; Gabriel M Simon; Esther K Kemper; Michael R Lazear; Sifei Yin; Megan M Blewett; Melissa M Dix; Nhan Nguyen; Maxim N Shokhirev; Emily N Chin; Luke L Lairson; Bruno Melillo; Stuart L Schreiber; Stefano Forli; John R Teijaro; Benjamin F Cravatt
Journal:  Cell       Date:  2020-07-29       Impact factor: 41.582

10.  Structural and Functional Insights into PpgL, a Metal-Independent β-Propeller Gluconolactonase That Contributes to Pseudomonas aeruginosa Virulence.

Authors:  Ying-Jie Song; Kai-Lun Wang; Ya-Lin Shen; Jie Gao; Tao Li; Yi-Bo Zhu; Chang-Cheng Li; Li-Hui He; Qiao-Xia Zhou; Ning-Lin Zhao; Chang Zhao; Jing Yang; Qin Huang; Xing-Yu Mu; Hong Li; Deng-Feng Dou; Chuan Liu; Jian-Hua He; Bo Sun; Rui Bao
Journal:  Infect Immun       Date:  2019-03-25       Impact factor: 3.441
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.