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 …

Solution pH is a critical environmental factor for chemical and biological processes. Over the
last decade, significant efforts have been made in the development of constant pH molecular …

Molecular dynamics (MD) computer simulations are used routinely to compute atomistic
trajectories of complex systems. Systems are simulated in various ensembles, depending on …

Constant pH molecular dynamics (MD) simulations sample protonation states on the fly
according to the conformational environment and user specified pH conditions; however, the …

The Alchemical Transfer Method (ATM) is herein validated against the relative binding-free
energies (RBFEs) of a diverse set of protein–ligand complexes. We employed a streamlined …

In this work, we deliver a proof of concept for a fast method that introduces pH effects into
classical coarse-grained (CG) molecular dynamics simulations. Our approach is based upon …

In drug discovery programs, modifications that change the net charge of the ligands are
often considered to improve the binding potency and solubility, or to address other …

Development of a pH stat to properly control solution pH in biomolecular simulations has
been a long-standing goal in the community. Toward this goal recent years have witnessed …

Building on the substantial progress that has been made in using free energy perturbation
(FEP) methods to predict the relative binding affinities of small molecule ligands to proteins …

Self-assembling polysaccharides can form complex networks with structures and properties
highly dependent on the sequence of triggering cues. Controlling the emergence of such …