AutoDockFR home page<\/h3>\n
This site is under active development to replace the legacy AutoDockFR site<\/a>.<\/strong><\/p>\n<\/div> AutoDockFR<\/em> (or\u00a0ADFR in short<\/em>) is a protein-ligand docking program<\/strong>\u00a0developed in the Sanner laboratory at Scripps Research under the AutoDock<\/em> umbrella.<\/p>\n It uses:<\/p>\n While it supports the docking modes available in AutoDock4<\/em> and Vina<\/em>, it was designed specifically, to include selective receptor flexibility<\/strong> and also supports covalent docking<\/strong>.Its custom Genetic Algorithm enables docking ligands with more rotatable bonds than AutoDock4<\/em>. It is distributed as part of the ADFR<\/em> software suite<\/a> which provides additional\u00a0 tools facilitating automated docking.<\/p>\n Ease of use<\/strong><\/p>\n ADFR<\/em>\u00a0implements several features that help streamlines the docking procedure, and support the management and reproducibility of docking experiments through data-provenance. Self-documented files are used for storing: i<\/em>) binding pocket representation used for docking (i.e.<\/em>\u00a0.trg\u00a0target files<\/strong>), and ii)<\/em> docking results (.dro Docking Results Object files<\/strong>). The meta-data stored in these files support not only supports reproducibility, but also reduces risks of operator errors, such as\u00a0mixing up affinity maps.<\/p>\n Input<\/strong><\/p>\n ADFR read ligands<\/strong>\u00a0prepared for docking with AutoDock,\u00a0i.e.<\/em> in the PDBQT format and organize the reflect ligand flexibility based on rotatable bonds. A PDBQT file can be generated from a pdb file of a ligand using the prepare_ligand<\/em>.<\/p>\n The receptor<\/strong> is specified as a target file, i.e.<\/em> a single file describing the receptor. Target files can be calculated for a receptor in the PDBQT file format from the command using the agfr<\/em><\/strong> program, or using the graphical user interface agfrgui<\/strong><\/em>.\u00a0A PDBQT file can be generated from a pdb file of a receptor using the prepare_receptor<\/em> from the ADFR<\/em> suite.<\/p>\n Usage<\/strong><\/p>\n given a receptor and a ligand prepared for docking with AutoDock <\/em>(i.e.<\/em> in PDBQT format), a simple docking can be performed as follows:<\/p>\n![](\"https:\/\/ccsb.scripps.edu\/adfr\/wp-content\/uploads\/sites\/36\/2019\/04\/Screen-Shot-2019-04-18-at-2.09.50-PM.png\" "\\"Screen")
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