Abstract The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages that have …

Protein preparation is a critical step in molecular simulations that consists of refining a
Protein Data Bank (PDB) structure by assigning titration states and optimizing the hydrogen …

Peptides and proteins protonation equilibrium is strongly influenced by its surrounding
media. Remarkably, until now, there have been no quantitative and systematic studies …

Monte Carlo (MC) methods are important computational tools for molecular structure
optimizations and predictions. When solvent effects are explicitly considered, MC methods …

Current constant-pH molecular dynamics (CpHMD) simulations provide a proper treatment
of pH effects on the structure and dynamics of soluble biomolecules like peptides and …

Electrostatic interactions among colloidal particles are often described using the venerable
(two-particle) Derjaguin–Landau–Verwey–Overbeek (DLVO) approximation and its various …

In protein crystallization, precipitants are used to control the final protein concentration in the
solution and/or to decrease the protein solubility for nucleation and growth. In this study, we …