Literature DB >> 14696075

Automated docking of highly flexible ligands by genetic algorithms: a critical assessment.

Marco Cecchini1, Peter Kolb, Nicolas Majeux, Amedeo Caflisch.   

Abstract

An improved version of the fragment-based flexible ligand docking approach SEED-FFLD is tested on inhibitors of human immunodeficiency virus type 1 protease, human alpha-thrombin and the estrogen receptor beta. The docking results indicate that it is possible to correctly reproduce the binding mode of inhibitors with more than ten rotatable bonds if the strain in their covalent geometry upon binding is not large. A high degree of convergence towards a unique binding mode in multiple runs of the genetic algorithm is proposed as a necessary condition for successful docking. Copyright 2003 Wiley Periodicals, Inc.

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Year:  2004        PMID： 14696075     DOI： 10.1002/jcc.10384

Source DB:  PubMed          Journal:  J Comput Chem        ISSN： 0192-8651            Impact factor:   3.376


  10 in total

1.  In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety.

Authors:  Rajkumar Ganesan; Stjepan Jelakovic; Peer R E Mittl; Amedeo Caflisch; Markus G Grütter
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-07-13

2.  Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach.

Authors:  Hao-Yang Liu; Xiaoqin Zou
Journal:  J Phys Chem B       Date:  2006-05-11       Impact factor: 2.991

3.  Ligand Strain Energy in Large Library Docking.

Authors:  Shuo Gu; Matthew S Smith; Ying Yang; John J Irwin; Brian K Shoichet
Journal:  J Chem Inf Model       Date:  2021-09-01       Impact factor: 6.162

4.  A double-headed cathepsin B inhibitor devoid of warhead.

Authors:  Patricia Schenker; Pietro Alfarano; Peter Kolb; Amedeo Caflisch; Antonio Baici
Journal:  Protein Sci       Date:  2008-09-16       Impact factor: 6.725

Review 5.  Advances and challenges in protein-ligand docking.

Authors:  Sheng-You Huang; Xiaoqin Zou
Journal:  Int J Mol Sci       Date:  2010-08-18       Impact factor: 5.923

6.  Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance.

Authors:  Ludovic Chaput; Juan Martinez-Sanz; Nicolas Saettel; Liliane Mouawad
Journal:  J Cheminform       Date:  2016-10-17       Impact factor: 5.514

7.  Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds.

Authors:  Ludovic Chaput; Liliane Mouawad
Journal:  J Cheminform       Date:  2017-06-12       Impact factor: 5.514

8.  Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking.

Authors:  Dariusz Ekonomiuk; Xun-Cheng Su; Kiyoshi Ozawa; Christophe Bodenreider; Siew Pheng Lim; Zheng Yin; Thomas H Keller; David Beer; Viral Patel; Gottfried Otting; Amedeo Caflisch; Danzhi Huang
Journal:  PLoS Negl Trop Dis       Date:  2009-01-13

9.  LIBSA--a method for the determination of ligand-binding preference to allosteric sites on receptor ensembles.

Authors:  Harrison J Hocker; Nandini Rambahal; Alemayehu A Gorfe
Journal:  J Chem Inf Model       Date:  2014-01-30       Impact factor: 4.956

10.  Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.

Authors:  Vincent Zoete; Thierry Schuepbach; Christophe Bovigny; Prasad Chaskar; Antoine Daina; Ute F Röhrig; Olivier Michielin
Journal:  J Comput Chem       Date:  2015-11-12       Impact factor: 3.376
  10 in total

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