Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …

Ensemble docking corresponds to the generation of an" ensemble" of drug target
conformations in computational structure-based drug discovery, often obtained by using …

Molecular dynamics (MD) allows the study of biological and chemical systems at the
atomistic level on timescales from femtoseconds to milliseconds. It complements experiment …

This study describes the effect of temperature on binding parameters as well as mode of
binding between coumarin 152 (C152) and human serum albumin (HSA). Site marker …

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal
antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is …

A new version of the coarse-grained (CG) SIRAH force field for proteins has been
developed. Modifications to bonded and non-bonded interactions on the existing molecular …

Molecular dynamics simulation is now a widespread approach for understanding complex
systems on the atomistic scale. It finds applications from physics and chemistry to …