Automated, high-throughput docking of small molecules vs. macromolecular targets for applications in combinatorial chemistry, virtual library screening and design, and target identification. DockIt rapidly docks small ligands with complete conformational flexibility into a binding site.
Small molecule databases can be screened without needing to precalculate 3D-coordinates, since only a 2D SMILES representation of the small molecule is required.
DockIt extends Daylight's Rubicon SMARTS rule-based method, which calculates random, sterically allowed conformers, to docking.
DockIt generates conformations directly into binding site spheres using distance geometry for intraligand and ligand-sphere interactions, followed by a simple molecular mechanics approach (or other functions) for ligand-site interactions.
Several user-selectable scoring functions are provided for ranking docked molecules.
DockIt requires .5 to 1 minute per molecule. Up to 100 random trials are required for small molecules (< 50 nonhydrogen atoms).