Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics,
including electronic polarization. Due to recent advances in physical models, simulation …

Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …

Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

Development of the AMOEBA (atomic multipole optimized energetics for biomolecular
simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes …

The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence
and electrostatic parameters were determined from high-level quantum mechanical data …

Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …

Molecular force fields have been approaching a generational transition over the past several
years, moving away from well-established and well-tuned, but intrinsically limited, fixed point …

Accurate prediction of binding affinities has been a central goal of computational chemistry
for decades, yet remains elusive. Despite good progress, the required accuracy for use in a …

The ability to predict the mechanisms and the associated rate constants of protein–ligand
unbinding is of great practical importance in drug design. In this work we demonstrate how a …