Literature DB >> 23151798

What in silico molecular docking can do for the 'bench-working biologists'.

Marius Mihăşan1.   

Abstract

Required by an increasing amount of scientists, the in silico docking field is in full expansion, new algorithms and methods appearing at an exponential rate. The sheer range of available programs is overwhelming for the benchworking biologist, which is often discouraging by the lack of a graphical user interface, good user manual or literature to validate a given program. This mini-review attempts to present the docking problem and available solutions from a non-bioinformatician point of view and makes a selection of the available servers and programs. These tools are evaluated from several points of view, as numbers of citations, ease of usage and computer requirements. Finally, the capabilities and limitations as well as specific applications of in silico docking techniques are presented.

Mesh:

Year:  2012        PMID: 23151798     DOI: 10.1007/s12038-012-9273-8

Source DB:  PubMed          Journal:  J Biosci        ISSN: 0250-5991            Impact factor:   1.826


  59 in total

1.  ZDOCK: an initial-stage protein-docking algorithm.

Authors:  Rong Chen; Li Li; Zhiping Weng
Journal:  Proteins       Date:  2003-07-01

2.  CAPRI: a Critical Assessment of PRedicted Interactions.

Authors:  Joël Janin; Kim Henrick; John Moult; Lynn Ten Eyck; Michael J E Sternberg; Sandor Vajda; Ilya Vakser; Shoshana J Wodak
Journal:  Proteins       Date:  2003-07-01

3.  Guided docking: first step to locate potential binding sites.

Authors:  Paul W Fitzjohn; Paul A Bates
Journal:  Proteins       Date:  2003-07-01

4.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.

Authors:  Thomas A Halgren; Robert B Murphy; Richard A Friesner; Hege S Beard; Leah L Frye; W Thomas Pollard; Jay L Banks
Journal:  J Med Chem       Date:  2004-03-25       Impact factor: 7.446

5.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Authors:  Richard A Friesner; Jay L Banks; Robert B Murphy; Thomas A Halgren; Jasna J Klicic; Daniel T Mainz; Matthew P Repasky; Eric H Knoll; Mee Shelley; Jason K Perry; David E Shaw; Perry Francis; Peter S Shenkin
Journal:  J Med Chem       Date:  2004-03-25       Impact factor: 7.446

Review 6.  Structure-based strategies for drug design and discovery.

Authors:  I D Kuntz
Journal:  Science       Date:  1992-08-21       Impact factor: 47.728

7.  Soft docking and multiple receptor conformations in virtual screening.

Authors:  Anna Maria Ferrari; Binqing Q Wei; Luca Costantino; Brian K Shoichet
Journal:  J Med Chem       Date:  2004-10-07       Impact factor: 7.446

Review 8.  Comparing protein-ligand docking programs is difficult.

Authors:  Jason C Cole; Christopher W Murray; J Willem M Nissink; Richard D Taylor; Robin Taylor
Journal:  Proteins       Date:  2005-08-15

9.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.

Authors:  Richard A Friesner; Robert B Murphy; Matthew P Repasky; Leah L Frye; Jeremy R Greenwood; Thomas A Halgren; Paul C Sanschagrin; Daniel T Mainz
Journal:  J Med Chem       Date:  2006-10-19       Impact factor: 7.446

10.  CoMFA, LeapFrog and blind docking studies on sulfonanilide derivatives acting as selective aromatase expression regulators.

Authors:  Carlos Gueto; Juan Torres; Ricardo Vivas-Reyes
Journal:  Eur J Med Chem       Date:  2009-02-15       Impact factor: 6.514

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  8 in total

Review 1.  Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.

Authors:  J V Vermaas; N Trebesch; C G Mayne; S Thangapandian; M Shekhar; P Mahinthichaichan; J L Baylon; T Jiang; Y Wang; M P Muller; E Shinn; Z Zhao; P-C Wen; E Tajkhorshid
Journal:  Methods Enzymol       Date:  2016-07-11       Impact factor: 1.600

Review 2.  Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators.

Authors:  Daniel Şterbuleac
Journal:  RSC Med Chem       Date:  2021-07-22

3.  Molecular Characterization and Computational Modelling of New Delhi Metallo-β-Lactamase-5 from an Escherichia coli Isolate (KOEC3) of Bovine Origin.

Authors:  D Purkait; A Ahuja; U Bhattacharjee; A Singha; K Rhetso; T K Dey; S Das; R K Sanjukta; K Puro; I Shakuntala; A Sen; A Banerjee; I Sharma; R S Bhatta; M Mawlong; C Guha; N R Pradhan; S Ghatak
Journal:  Indian J Microbiol       Date:  2016-02-11       Impact factor: 2.461

Review 4.  Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Authors:  Saher A Shaikh; Jing Li; Giray Enkavi; Po-Chao Wen; Zhijian Huang; Emad Tajkhorshid
Journal:  Biochemistry       Date:  2013-01-17       Impact factor: 3.162

5.  Artemisinin Derivatives Target Topoisomerase 1 and Cause DNA Damage in Silico and in Vitro.

Authors:  Onat Kadioglu; Ariel Chan; Alena Cong Ling Qiu; Vincent Kam Wai Wong; Vanessa Colligs; Sabine Wecklein; Halima Freund-Henni Rached; Thomas Efferth; Wen-Luan Wendy Hsiao
Journal:  Front Pharmacol       Date:  2017-10-09       Impact factor: 5.810

6.  Venus Flytrap (Dionaea muscipula Solander ex Ellis) Contains Powerful Compounds that Prevent and Cure Cancer.

Authors:  François Gaascht; Mario Dicato; Marc Diederich
Journal:  Front Oncol       Date:  2013-08-20       Impact factor: 6.244

7.  Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations.

Authors:  Qifeng Bai; Yonghua Shao; Dabo Pan; Yang Zhang; Huanxiang Liu; Xiaojun Yao
Journal:  PLoS One       Date:  2014-09-17       Impact factor: 3.240

8.  Flavonolignans inhibit the arachidonic acid pathway in blood platelets.

Authors:  Michal Bijak; Joanna Saluk-Bijak
Journal:  BMC Complement Altern Med       Date:  2017-08-10       Impact factor: 4.782

  8 in total

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