Automated, high-throughput docking of small molecules vs. macromolecular targets for applications in combinatorial chemistry, virtual library screening and design, and target identification. RubiconDock 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.
RubiconDock extends Daylight's Rubicon SMARTS rule-based method for calculating random, sterically allowed conformers to docking.
RubiconDock 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.
RubiconDock requires 1 to 1.5 minutes per molecule (SGI R10000): 2-4 random dockings are calculated per second; up to 100 random trials are required for small molecules (< 50 nonhydrogen atoms).