A high-throughput molecular docking facility is presented for screening combinatorial libraries to identity binding ligands and ultimately pharmaceutical compounds. The facility employs a pre-coking conformational search to generate multiple solution conformations of a ligand. The molecula r docking facility includes: generating a binding site image of the target molecule, the binding site image to atoms in at least one solution conformation of the multiple solution conformations of the ligand to obtain at least one ligand position relative to the target molecule in a ligand-target molecule complex formation; and optimizing the at least one ligand position while allowing translation, orientation and rotatable bonds of the ligand to vary, and while holding the target molecule fixed. Docking results are clustered using as a metric the rms deviation between the core of two docked molecules. A library is rated is rated as to complementarity to the target molecule according to the relative number of ligands in the top cluster.</SD OAB>
MOLECULAR DOCKING METHODS FOR ASSESSING COMPLEMENTARITY OF COMBINATORIAL LIBRARIES TO BIOTARGETS