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AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions.

ABSTRACT: SUMMARY:The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein-ligand interactions, such as known ligand pharmacophore or interaction sites derived from cosolvent molecular dynamics. AutoDock Bias is a straightforward and easy to use script-based method that allows the introduction of different types of user-defined biases for fine-tuning AutoDock4 docking calculations. AVAILABILITY AND IMPLEMENTATION:AutoDock Bias is distributed with MGLTools (since version 1.5.7), and freely available on the web at http://ccsb.scripps.edu/mgltools/ or http://autodockbias.wordpress.com. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Arcon JP

PROVIDER: S-EPMC6761960 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions.

Arcon Juan Pablo JP Modenutti Carlos P CP Avendaño Demian D Lopez Elias D ED Defelipe Lucas A LA Ambrosio Francesca Alessandra FA Turjanski Adrian G AG Forli Stefano S Marti Marcelo A MA

Bioinformatics (Oxford, England) 20191001 19

<h4>Summary</h4>The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein-ligand interactions, such as known ligand pharmacophore or interaction sites derived from cosolvent molecular dynamics. AutoDock Bias is a straightforward and easy to use script-based method that allows the introduction of different types of user-defined biases for fine-tuning AutoDock4 docking calculations.<h4 ...[more]

PMID: 30825370

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