Quantum Mechanics/Molecular Mechanics

Quantum Mechanics/Molecular Mechanics (QM/MM) is a multi-scale/multi-resolution computational chemistry method that treats different parts of the systems with different levels of calculations. Using the QM/MM molecular simulation method, Polaris combines the strengths of ab initio QM calculations (accuracy) and MM (speed) approaches. The QM/MM approach was introduced in the 1976 paper of Warshel and Levitt. They, along with Martin Karplus, won the 2013 Nobel Prize in Chemistry for "the development of multiscale models for complex chemical systems".


Polaris uses a fully atomistic simulation, with confirmation of multiple ligands bound to the  protein complex, that includes solvent, cofactors and ions to predict binding affinity. The binding affinity is evaluated using the

Taken from: Hatcher Frush, Sekharan, and Keinan, J. Phys. Chem. B 2017, 121, 8142−8148 DOI: 10.1021/acs.jpcb.7b07224

Linear Interaction Energy (LIE) formalism. Previously,  QM/MM methods have shown an 80% accuracy rate in predicting binding affinity.  Using the  Tachyontm, system, these calculations can be  executed in an embarrassingly parallel manner on multiple cloud environments. This means that Polarisqb will be able to use these proven methods (LIE QM/MM) of molecular drug design on a fully quantum, system agnostic platform.