ASEDock -- Database Searching of Ligands and Receptors Based on Alpha Spheres and Excluded Volumes

Abstract

A new docking program, ASEDock, is developed and tested in searching the receptor that could favorably be docked by the query ligand using the testset of the 50 highly resolved complexes selected from PDB. Since it makes good use of Gaussian-type function for evaluating and optimizing the overlap between ligands and site model, it can pose ligands onto the docking site relatively faster and more effectively than using potential energy functions. The fitness after posing is scored by the the overlapping fitness score and pKi derived by fitting the hydrogen-bonds, the hydrophobic contacts, and the entropy changes to the reported pKi's of the complexes in PDB. ASEDock reproduced the original ligand-receptor complexes, and, furthermore, revealed possible pairs that could dock with each other to form stable complexes. Therefore, it could be useful in elucidating the receptors that could be influenced by the binding of query ligands and detect possible side effects by the virtual screening with ASEDock.