Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Metabolic alterations in the microenvironment significantly modulate tumor
immunosensitivity, but the underlying mechanisms remain obscure. Here, we report that …

INTRODUCTION Statistical mechanics aims to compute the average behavior of physical
systems on the basis of their microscopic constituents. For example, what is the probability …

The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic
and inactive heterochromatic regions of the genome,. In conventional nuclei, microscopy …

Cellular processes often depend on interactions between proteins and the formation of
macromolecular complexes. The impairment of such interactions can lead to deregulation of …

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It
allows users to easily add new features, including forces with novel functional forms, new …

The accurate calculation of protein/nucleic acid–ligand interactions or condensed phase
properties by force field-based methods require a precise description of the energetics of …

The all-atom additive CHARMM36 protein force field is widely used in molecular modeling
and simulations. We present its refinement, CHARMM36m (http://mackerell. umaryland …

The Tinker software, currently released as version 8, is a modular molecular mechanics and
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …