title: Survey of public domain software for docking simulations and virtual screening.
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.
authors.affiliation: Biomedical Informatics, Children's Hospital Research Foundation, Cincinnati, OH 45229, USA.
authors.forename: Jacek
authors.initials: J
authors.lastname: Biesiada
authors.forename: Aleksey
authors.initials: A
authors.lastname: Porollo
authors.forename: Prakash
authors.initials: P
authors.lastname: Velayutham
authors.forename: Michal
authors.initials: M
authors.lastname: Kouril
authors.forename: Jaroslaw
authors.initials: J
authors.lastname: Meller
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D045166:Estradiol Congeners / Q000737:chemistry; D047628:Estrogen Receptor alpha / Q000737:chemistry; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D045166:Estradiol Congeners; D047628:Estrogen Receptor alpha; D008024:Ligands; D011506:Proteins