Literature DB >> 21532931

Virtual Screening with AutoDock: Theory and Practice.

Sandro Cosconati1, Stefano Forli, Alex L Perryman, Rodney Harris, David S Goodsell, Arthur J Olson.   

Abstract

IMPORTANCE TO THE FIELD: Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules. AREAS COVERED IN THIS REVIEW: We describe virtual screening methods that are available in the AutoDock suite of programs, and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery. WHAT THE READER WILL GAIN: A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges. TAKE HOME MESSAGE: Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening.

Entities:  

Year:  2010        PMID： 21532931      PMCID： PMC3083070          DOI： 10.1517/17460441.2010.484460

Source DB:  PubMed          Journal:  Expert Opin Drug Discov        ISSN： 1746-0441            Impact factor:   6.098


  53 in total

Review 1.  Molecular recognition and docking algorithms.

Authors:  Natasja Brooijmans; Irwin D Kuntz
Journal:  Annu Rev Biophys Biomol Struct       Date:  2003-01-28

2.  Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients.

Authors:  Xin Chen; Charles H Reynolds
Journal:  J Chem Inf Comput Sci       Date:  2002 Nov-Dec

Review 3.  A review of protein-small molecule docking methods.

Authors:  R D Taylor; P J Jewsbury; J W Essex
Journal:  J Comput Aided Mol Des       Date:  2002-03       Impact factor: 3.686

4.  A 'rule of three' for fragment-based lead discovery?

Authors:  Miles Congreve; Robin Carr; Chris Murray; Harren Jhoti
Journal:  Drug Discov Today       Date:  2003-10-01       Impact factor: 7.851

5.  Ligand efficiency: a useful metric for lead selection.

Authors:  Andrew L Hopkins; Colin R Groom; Alexander Alex
Journal:  Drug Discov Today       Date:  2004-05-15       Impact factor: 7.851

6.  "In situ cross-docking" to simultaneously address multiple targets.

Authors:  Christoph A Sotriffer; Ingo Dramburg
Journal:  J Med Chem       Date:  2005-05-05       Impact factor: 7.446

Review 7.  Docking and scoring--theoretically easy, practically impossible?

Authors:  B Coupez; R A Lewis
Journal:  Curr Med Chem       Date:  2006       Impact factor: 4.530

8.  Virtual screening of human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase against the NCI diversity set by use of AutoDock to identify novel nonfolate inhibitors.

Authors:  Chenglong Li; Lan Xu; Dennis W Wolan; Ian A Wilson; Arthur J Olson
Journal:  J Med Chem       Date:  2004-12-30       Impact factor: 7.446

9.  Stabilizers of the Max homodimer identified in virtual ligand screening inhibit Myc function.

Authors:  Hao Jiang; Kristen E Bower; Albert E Beuscher; Bin Zhou; Andrey A Bobkov; Arthur J Olson; Peter K Vogt
Journal:  Mol Pharmacol       Date:  2009-06-04       Impact factor: 4.436

10.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.

Authors:  Garrett M Morris; Ruth Huey; William Lindstrom; Michel F Sanner; Richard K Belew; David S Goodsell; Arthur J Olson
Journal:  J Comput Chem       Date:  2009-12       Impact factor: 3.376
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  100 in total

1.  A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.

Authors:  Stefano Forli; Arthur J Olson
Journal:  J Med Chem       Date:  2012-01-13       Impact factor: 7.446

2.  Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks.

Authors:  Zhiqiang Yan; Jin Wang
Journal:  J Comput Aided Mol Des       Date:  2016-02-15       Impact factor: 3.686

3.  Molecular insight into substrate recognition and catalysis of Baeyer-Villiger monooxygenase MtmOIV, the key frame-modifying enzyme in the biosynthesis of anticancer agent mithramycin.

Authors:  Mary A Bosserman; Theresa Downey; Nicholas Noinaj; Susan K Buchanan; Jürgen Rohr
Journal:  ACS Chem Biol       Date:  2013-09-13       Impact factor: 5.100

4.  Response surface methodology in docking study of small molecule BACE-1 inhibitors.

Authors:  Nima Razzaghi-Asl; Ahmad Ebadi; Najmeh Edraki; Ahmadreza Mehdipour; Sara Shahabipour; Ramin Miri
Journal:  J Mol Model       Date:  2012-05-13       Impact factor: 1.810

5.  A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA.

Authors:  Alexander L Perryman; Weixuan Yu; Xin Wang; Sean Ekins; Stefano Forli; Shao-Gang Li; Joel S Freundlich; Peter J Tonge; Arthur J Olson
Journal:  J Chem Inf Model       Date:  2015-02-17       Impact factor: 4.956

6.  Docking and molecular dynamics studies on triclosan derivatives binding to FabI.

Authors:  Xuyun Yang; Junrui Lu; Ming Ying; Jiangbei Mu; Peichun Li; Yue Liu
Journal:  J Mol Model       Date:  2017-01-07       Impact factor: 1.810

7.  Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.

Authors:  Emilio Gallicchio; Nanjie Deng; Peng He; Lauren Wickstrom; Alexander L Perryman; Daniel N Santiago; Stefano Forli; Arthur J Olson; Ronald M Levy
Journal:  J Comput Aided Mol Des       Date:  2014-02-07       Impact factor: 3.686

8.  The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators.

Authors:  Mutasem O Taha; Maha Habash; Mohammad A Khanfar
Journal:  J Comput Aided Mol Des       Date:  2014-03-08       Impact factor: 3.686

9.  Neuroprotection of Andrographolide Against Microglia-Mediated Inflammatory Injury and Oxidative Damage in PC12 Neurons.

Authors:  Yuanzhen Xu; Dan Tang; Jianping Wang; Hongbo Wei; Jinming Gao
Journal:  Neurochem Res       Date:  2019-09-27       Impact factor: 3.996

10.  Identification, modeling and ligand affinity of early deuterostome CYP51s, and functional characterization of recombinant zebrafish sterol 14α-demethylase.

Authors:  Ann Michelle Stanley Morrison; Jared V Goldstone; David C Lamb; Akira Kubota; Benjamin Lemaire; John J Stegeman
Journal:  Biochim Biophys Acta       Date:  2013-12-19
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