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 …

Abstract The pKa Cooperative (http://www. pkacoop. org) was organized to advance
development of accurate and useful computational methods for structure‐based calculation …

ABSTRACT pH is a ubiquitous regulator of biological activity, including protein‐folding,
protein‐protein interactions, and enzymatic activity. Existing constant pH molecular …

A computational method is developed to carry out explicit solvent simulations of complex
molecular systems under conditions of constant pH. In constant-pH simulations, preidentified …

The behavior of proteins is closely related to the protonation states of the residues.
Therefore, prediction and measurement of pKa are essential to understand the basic …

Protonation states of ionizable protein residues modulate many essential biological
processes. For correct modeling and understanding of these processes, it is crucial to …

In this work, we apply the recently developed constant pH molecular dynamics technique to
study protonation equilibria of titratable side chains in the context of simple transmembrane …

Structural consequences of ionization of residues buried in the hydrophobic interior of
proteins were examined systematically in 25 proteins with internal Lys residues. Crystal …

To probe the microscopic mechanisms that govern the titration behavior of buried ionizable
groups, microsecond explicit solvent molecular dynamics simulations are carried out for …

The rational modification of protein stability is an important goal of protein design. Protein
surface electrostatic interactions are not evolutionarily optimized for stability and are an …