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Bioinformatics Advance Access published online on May 23, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl197
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 27, 2006
Revised May 11, 2006
Accepted May 17, 2006

Applications note

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

Montserrat Vaqué 1, Anna Arola 1, Carles Aliagas 2, and Gerard Pujadas 3 *

1 Departament de Bioquímica i Biotecnologia, C/Marcel·lí Domingo s/n, Av. Països Catalans, 26. Universitat Rovira i Virgili, Campus de Sant Pere Sescelades, Tarragona 43007, Catalonia (Spain)
2 Departament d'Enginyeria Informàtica i Matemàtiques, Av. Països Catalans, 26. Universitat Rovira i Virgili, Campus de Sant Pere Sescelades, Tarragona 43007, Catalonia (Spain)
3 Departament de Bioquímica i Biotecnologia, C/ Marcel·lí Domingo s/n, Av. Països Catalans, 26. Universitat Rovira i Virgili, Campus de Sant Pere Sescelades, Tarragona 43007, Catalonia (Spain)

* To whom correspondence should be addressed.
Gerard Pujadas, E-mail: gerard.pujadas{at}urv.cat


  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.

Supplementary information: http://www.quimica.urv.cat/~pujadas/BDT/.

Associate Editor: Martin Bishop
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