Literature DB >> 16720587

BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock.

Montserrat Vaqué1, Anna Arola, Carles Aliagas, Gerard Pujadas.   

Abstract

MOTIVATION: AutoGrid/AutoDock is one of the most popular software packages for docking, but its automation is not trivial for tasks such as (1) the virtual screening of a library of ligands against a set of possible receptors; (2) the use of receptor flexibility and (3) making a blind-docking experiment with the whole receptor surface. This is an obstacle for research teams in the fields of Chemistry and the Life Sciences who are interested in conducting this kind of experiment but do not have enough programming skills. To overcome these limitations, we have designed BDT, an easy-to-use graphic interface for AutoGrid/AutoDock. AVAILABILITY: BDT is available for free, upon request, for non-commercial research.

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Year:  2006        PMID： 16720587     DOI： 10.1093/bioinformatics/btl197

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

1.  VSDMIP: virtual screening data management on an integrated platform.

Authors:  Rubén Gil-Redondo; Jorge Estrada; Antonio Morreale; Fernando Herranz; Javier Sancho; Angel R Ortiz
Journal:  J Comput Aided Mol Des       Date:  2008-10-22       Impact factor: 3.686

2.  VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface.

Authors:  Álvaro Cortés Cabrera; Rubén Gil-Redondo; Almudena Perona; Federico Gago; Antonio Morreale
Journal:  J Comput Aided Mol Des       Date:  2011-08-09       Impact factor: 3.686

3.  Ligand docking and binding site analysis with PyMOL and Autodock/Vina.

Authors:  Daniel Seeliger; Bert L de Groot
Journal:  J Comput Aided Mol Des       Date:  2010-04-17       Impact factor: 3.686

4.  MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters.

Authors:  Rui Mv Abreu; Hugo Jc Froufe; Maria João Rp Queiroz; Isabel Cfr Ferreira
Journal:  J Cheminform       Date:  2010-10-28       Impact factor: 5.514

5.  idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach.

Authors:  Jui-Chih Wang; Pei-Ying Chu; Chung-Ming Chen; Jung-Hsin Lin
Journal:  Nucleic Acids Res       Date:  2012-05-30       Impact factor: 16.971

6.  Accessible high-throughput virtual screening molecular docking software for students and educators.

Authors:  Reed B Jacob; Tim Andersen; Owen M McDougal
Journal:  PLoS Comput Biol       Date:  2012-05-31       Impact factor: 4.475

7.  SPIDR: small-molecule peptide-influenced drug repurposing.

Authors:  Matthew D King; Thomas Long; Daniel L Pfalmer; Timothy L Andersen; Owen M McDougal
Journal:  BMC Bioinformatics       Date:  2018-04-16       Impact factor: 3.169

8.  DOVIS: an implementation for high-throughput virtual screening using AutoDock.

Authors:  Shuxing Zhang; Kamal Kumar; Xiaohui Jiang; Anders Wallqvist; Jaques Reifman
Journal:  BMC Bioinformatics       Date:  2008-02-27       Impact factor: 3.169

9.  AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4.

Authors:  Mario S Valdés-Tresanco; Mario E Valdés-Tresanco; Pedro A Valiente; Ernesto Moreno
Journal:  Biol Direct       Date:  2020-09-16       Impact factor: 4.540
  9 in total

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