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

Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …

MM-PBSA is a post-processing end-state method to calculate free energies of molecules in
solution. MMPBSA. py is a program written in Python for streamlining end-state free energy …

By using different evaluation strategies, we systemically evaluated the performance of
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …

The Molecular Mechanics/Poisson− Boltzmann Surface Area (MM/PBSA) and the Molecular
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …

OpenMM is a software toolkit for performing molecular simulations on a range of high
performance computing architectures. It is based on a layered architecture: the lower layers …

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 …

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 …