DockIt is a set of programs for docking small molecules into macromolecules. See the DockIt page for an introduction and installation instructions.
select protein with (optionally) metals and relevant waters and ligand from PDB file.
generate spheres filling potential protein binding sites
score, select and cluster spheres most likely to represent binding site(s).
convert protein and ligand PDB files to CEX and assign partial charges.
assign partial charges to protein or ligand atoms by SMARTS rules
assign PMF atom types to ligand and protein
assign PLP atom types to ligand and protein
distance geometry + sphere docking engine
rescores docked structures with PMF, PLP No longer needed as of DockIt 1.5 since rescoring is done during dock.
How to use the plug in scoring functions. Documentation on how to add new scoring functions to DockIt.
Hints and troubleshooting tips for using DockIt.
