BDT: an Easy-to-use Front-end Application for Automation of Massive Docking Tasks and Complex Docking Strategies with AutoDock

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2006 May 25

PMID 16720587

Citations 10

Authors

Montserrat Vaque

Anna Arola

Carles Aliagas

Gerard Pujadas

Affiliations

Soon will be listed here.

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.

Citing Articles

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

Valdes-Tresanco M, Valdes-Tresanco M, Valiente P, Moreno E Biol Direct. 2020; 15(1):12.

PMID: 32938494 PMC: 7493944. DOI: 10.1186/s13062-020-00267-2.

AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools.

Zhang Y, Forli S, Omelchenko A, Sanner M J Comput Chem. 2019; 40(32):2882-2886.

PMID: 31436329 PMC: 7737998. DOI: 10.1002/jcc.26054.

SPIDR: small-molecule peptide-influenced drug repurposing.

King M, Long T, Pfalmer D, Andersen T, McDougal O BMC Bioinformatics. 2018; 19(1):138.

PMID: 29661129 PMC: 5902895. DOI: 10.1186/s12859-018-2153-y.

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

Jacob R, Andersen T, McDougal O PLoS Comput Biol. 2012; 8(5):e1002499.

PMID: 22693435 PMC: 3364939. DOI: 10.1371/journal.pcbi.1002499.

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

Wang J, Chu P, Chen C, Lin J Nucleic Acids Res. 2012; 40(Web Server issue):W393-9.

PMID: 22649057 PMC: 3394295. DOI: 10.1093/nar/gks496.