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Open Access Software review

Survey of public domain software for docking simulations and virtual screening

Jacek Biesiada12, Aleksey Porollo3, Prakash Velayutham1, Michal Kouril1 and Jaroslaw Meller134*

Author Affiliations

1 Biomedical Informatics, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA

2 Division of Management and Informatics, Technical University of Silesia, 40-819 Katowice, Poland

3 Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45226, USA

4 Department of Informatics, Nicholas Copernicus University, 87-100 Torun, Poland

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Human Genomics 2011, 5:497-505  doi:10.1186/1479-7364-5-5-497

Published: 1 July 2011

Abstract

Progress in functional genomics and structural studies on biological macromolecules are generating a growing number of potential targets for therapeutics, adding to the importance of computational approaches for small molecule docking and virtual screening of candidate compounds. In this review, recent improvements in several public domain packages that are widely used in the context of drug development, including DOCK, AutoDock, AutoDock Vina and Screening for Ligands by Induced-fit Docking Efficiently (SLIDE) are surveyed. The authors also survey methods for the analysis and visualisation of docking simulations, as an important step in the overall assessment of the results. In order to illustrate the performance and limitations of current docking programs, the authors used the National Center for Toxicological Research (NCTR) oestrogen receptor benchmark set of 232 oestrogenic compounds with experimentally measured strength of binding to oestrogen receptor alpha. The methods tested here yielded a correlation coefficient of up to 0.6 between the predicted and observed binding affinities for active compounds in this benchmark.

Keywords:
drug discovery; small molecule docking; virtual screening; docking packages; visualisation of docking poses; oestrogen receptor; oestrogen activity prediction; SAR