Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …

Computer-aided drug discovery/design methods have played a major role in the
development of therapeutically important small molecules for over three decades. These …

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

Over the past decade, the Rosetta biomolecular modeling suite has informed diverse
biological questions and engineering challenges ranging from interpretation of low …

This review on continuum solvation models has been preceded in Chemical Reviews by
others addressing the same subject. They are due to Tomasi and Persico1 (published in …

We describe the development, current features, and some directions for future development
of the Amber package of computer programs. This package evolved from a program that was …

We discuss basic physical–chemical principles underlying the formation of stable
macromolecular complexes, which in many cases are likely to be the biological units …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …

Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …