This article recapitulates the state of the art regarding simulations of ionization equilibria of
weak polyelectrolyte solutions and gels. We start out by reviewing the essential …

Dendrimers are an excellent candidate that exhibits higher proficiency in biomedical
applications such as drug delivery, inhibition and/or targeting gene delivery. The use of …

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 …

The protonation of titratable residues has a significant impact on the structure and function of
biomolecules, influencing many physicochemical and ADME properties. Thus, the …

With the recent increase in computing power, the molecular modeling community is now
more focused on improving the accuracy and overall quality of biomolecular simulations. For …

We have designed a protocol combining constant-pH molecular dynamics (CpHMD)
simulations with an umbrella sampling (US) scheme (US-CpHMD) to study the mechanism …

Existing computational methods for estimating p K a values in proteins rely on theoretical
approximations and lengthy computations. In this work, we use a data set of 6 million …

Although epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs)-based
molecular targeted therapy are proved to be effective in the treatment of non-small cell lung …

Protein–protein association is often mediated by electrostatic interactions and modulated by
pH. However, experimental and computational studies have often overlooked the effect of …

The impact of pH on proteins is significant but often neglected in molecular dynamics
simulations. Constant-pH Molecular Dynamics (CpHMD) is the state-of-the-art methodology …