Applications of Integrated Molecular Dynamics and Fragment Molecular Orbital (MD+FMO) Calculations in Drug Discovery and Structural Biology.

By integrating the fragment molecular orbital (FMO) method, a quantum chemical calculation approach, with classical molecular dynamics (MD) simulations, the MD+FMO framework extends interaction analysis beyond a single static structure to enable quantitative structure-activity relationship evaluation across diverse scaffolds, pose estimation for complexes with unknown structures, and investigation of molecular recognition mechanisms in mutant proteins. This chapter summarizes current evaluation strategies using the MD+FMO approach and integration with diverse experimental techniques, highlighting its value as an analytical method that complements experimental studies in molecular biology.