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. Why use DockIt?
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 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.
User-selectable scoring functions are provided for
ranking docked molecules: Energy, PLP and PMF.
DockIt requires approximately 30 seconds per molecule.
DockIt is available in a parallel version (using PVM) which works
well for SMP or loosely coupled clusters.
For further information on DockIt, see the online documentation.