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