Survey of public domain software for docking simulations and virtual screening
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
Human Genomics 2011, 5:497-505 doi:10.1186/1479-7364-5-5-497Published: 1 July 2011
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.