Integrated modeling program, applied chemical theory (IMPACT)
JL Banks, HS Beard, Y Cao, AE Cho… - Journal of …, 2005 - Wiley Online Library
We provide an overview of the IMPACT molecular mechanics program with an emphasis on
recent developments and a description of its current functionality. With respect to core …
recent developments and a description of its current functionality. With respect to core …
Polarization effects in molecular mechanical force fields
The focus here is on incorporating electronic polarization into classical molecular
mechanical force fields used for macromolecular simulations. First, we briefly examine …
mechanical force fields used for macromolecular simulations. First, we briefly examine …
Classical electrostatics for biomolecular simulations
Classical atomistic simulations, also known as molecular mechanics simulations, use simple
potential-energy functions to model molecular systems at the atomic level. In this …
potential-energy functions to model molecular systems at the atomic level. In this …
Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications
A current emphasis in empirical force fields is on the development of potential functions that
explicitly treat electronic polarizability. In the present article, the commonly used …
explicitly treat electronic polarizability. In the present article, the commonly used …
Polarizable force fields for molecular dynamics simulations of biomolecules
CM Baker - Wiley Interdisciplinary Reviews: Computational …, 2015 - Wiley Online Library
Molecular dynamics simulations are well established for the study of biomolecular systems.
Within these simulations, energy functions known as force fields are used to determine the …
Within these simulations, energy functions known as force fields are used to determine the …
Contribution of conformer focusing to the uncertainty in predicting free energies for protein− ligand binding
When a ligand binds to a protein, it is typically not in the lowest-energy conformation for the
unbound ligand and there is also a loss of conformational degrees of freedom. The free …
unbound ligand and there is also a loss of conformational degrees of freedom. The free …
Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs
The capabilities of the polarizable force fields for alchemical free energy calculations have
been limited by the high computational cost and complexity of the underlying potential …
been limited by the high computational cost and complexity of the underlying potential …