Literature DB >> 15723628

Docking: successes and challenges.

Venkatraman Mohan1, Alan C Gibbs, Maxwell D Cummings, Edward P Jaeger, Renee L DesJarlais.   

Abstract

The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Recent progress made in the development and application of methods to include target flexibility are summarized. The fundamental issues and challenges involved in comparing various docking methods are discussed. Limitations of current technologies as well as future prospects are presented.

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Year:  2005        PMID： 15723628     DOI： 10.2174/1381612053382106

Source DB:  PubMed          Journal:  Curr Pharm Des        ISSN： 1381-6128            Impact factor:   3.116


  43 in total

1.  Correlation between biological activity and binding energy in systems of integrin with cyclic RGD-containing binders: a QM/MM molecular dynamics study.

Authors:  Mingli Xiang; Yuchun Lin; Gu He; Lijuan Chen; Mingli Yang; Shengyong Yang; Yirong Mo
Journal:  J Mol Model       Date:  2012-06-27       Impact factor: 1.810

2.  Benchmarking sets for molecular docking.

Authors:  Niu Huang; Brian K Shoichet; John J Irwin
Journal:  J Med Chem       Date:  2006-11-16       Impact factor: 7.446

Review 3.  Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach.

Authors:  I M Kapetanovic
Journal:  Chem Biol Interact       Date:  2006-12-16       Impact factor: 5.192

Review 4.  From laptop to benchtop to bedside: structure-based drug design on protein targets.

Authors:  Lu Chen; John K Morrow; Hoang T Tran; Sharangdhar S Phatak; Lei Du-Cuny; Shuxing Zhang
Journal:  Curr Pharm Des       Date:  2012       Impact factor: 3.116

Review 5.  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

6.  Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?

Authors:  Andrew C Good; Tudor I Oprea
Journal:  J Comput Aided Mol Des       Date:  2008-01-09       Impact factor: 3.686

7.  Site-specific basicities regulate molecular recognition in receptor binding: in silico docking of thyroid hormones.

Authors:  Gergő Tóth; Ferenc Baska; András Schretner; Akos Rácz; Béla Noszál
Journal:  Eur Biophys J       Date:  2013-08-02       Impact factor: 1.733

8.  A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations.

Authors:  Bing Wang; Lance M Westerhoff; Kenneth M Merz
Journal:  J Med Chem       Date:  2007-09-15       Impact factor: 7.446

9.  Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors.

Authors:  Preyesh Stephen; Ramachandran Vijayan; Audesh Bhat; N Subbarao; R N K Bamezai
Journal:  J Comput Aided Mol Des       Date:  2007-08-21       Impact factor: 3.686

10.  Differences between high- and low-affinity complexes of enzymes and nonenzymes.

Authors:  Heather A Carlson; Richard D Smith; Nickolay A Khazanov; Paul D Kirchhoff; James B Dunbar; Mark L Benson
Journal:  J Med Chem       Date:  2008-10-01       Impact factor: 7.446
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