In the field of noncovalent interactions a new paradigm has recently become popular. It
stems from the analysis of molecular electrostatic potentials and introduces a label, which …

One of the largest challenges of computational chemistry is calculation of accurate free
energies for the binding of a small molecule to a biological macromolecule, which has …

TfCa, a promiscuous carboxylesterase from Thermobifida fusca, was found to hydrolyze
polyethylene terephthalate (PET) degradation intermediates such as bis (2-hydroxyethyl) …

We present an implementation of explicit solvent all atom classical molecular dynamics (MD)
within the AMBER program package that runs entirely on CUDA-enabled GPUs. First …

The utility of molecular dynamics (MD) simulations to model biomolecular structure,
dynamics, and interactions has witnessed enormous advances in recent years due to the …

We present an implementation of generalized Born implicit solvent all-atom classical
molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA …

Partition coefficients describe how a solute is distributed between two immiscible solvents.
They are used in drug design as a measure of a solute's hydrophobicity and a proxy for its …

Intrinsically disordered proteins (IDPs) or intrinsically disordered regions do not have a fixed
tertiary structure but play key roles in signal regulation, molecule recognition, and drug …

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al.
AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were …

The millisecond time scale needed for molecular dynamics simulations to approach the
quantitative study of protein folding is not yet routine. One approach to extend the simulation …