A molecular Docking program with Full Quantum Refinement (DFQR)

Site yet to come.
Comp. Theor. Chem. 1028 (2014), 7-18
AlgoGen is a program that greatly benefits from algorithmic advances in quantum chemistry. It is designed to perform (ligand) flexible molecular docking in order to ultimately pose a ligand in the receptor site by combining a quantum-chemistry method with a genetic algorithm (GA).

Thus, in contrast with regular program in the field of moleculat docking, this in-house software combines a classical level of theory and quantum chemistry; after exploring the best orientations of a ligand binding a host (Vina scoring), the best poses are automatically fully refined at the quantum chemistry level of theory using the semi-empirical quantum (SQM) PM7 method and the MOZYME function available in MOPAC2016.

AlgoGen is best suited to describe the charge polarization induced by the protein environment and also to account for possible charge-transfer (CT) interactions between a metal ion and the ligand during the docking process. Furthermore, it avoids the transferability problems that traditionally plague force field potential. There is no need to define special ligand parameters as long as the atoms are parameterized semi-empirically. Such a quantum–mechanical approach is unusual in the field of molecular docking. It remains, however, substantially much more CPU expensive than standard force field approaches.

AlgoGen is still under development. It will be soon made available freely for academic use upon request. Please, contact for details.