Many important protein functions are carried out through proton-coupled conformational
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …

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 …

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

Roughly half of the drug overdose-related deaths in the United States are related to
synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor …

DeepKa is a deep-learning-based protein p K a predictor proposed in our previous work. In
this study, a web server was developed that enables online protein p K a prediction driven …

Abstract The Na+/H+ exchanger SLC9B2, also known as NHA2, correlates with the long-
sought-after Na+/Li+ exchanger linked to the pathogenesis of diabetes mellitus and …

Cation/proton antiporters (CPAs) play a major role in maintaining living cells' homeostasis.
CPAs are commonly divided into two main groups, CPA1 and CPA2, and are further …

Permeability (P m) across biological membranes is of fundamental importance and a key
factor in drug absorption, distribution, and development. Although the majority of drugs will …

Classical molecular dynamics (MD) simulations provide unmatched spatial and time
resolution of protein structure and function. However, the accuracy of MD simulations often …

The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a
wide variety of ecological niches, from fermented foodstuffs to host-associated …