The present review is concerned with continuum and other implicit models of solvation
effects. We will concentrate on the elements required to make such models successful and …

Empirical force field‐based studies of biological macromolecules are becoming a common
tool for investigating their structure–activity relationships at an atomic level of detail. Such …

The Automated force field Topology Builder (ATB, http://compbio. biosci. uq. edu. au/atb) is a
Web-accessible server that can provide topologies and parameters for a wide range of …

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 …

Absolute binding free energy calculations and free energy decompositions are presented for
the protein–protein complexes H-Ras/C-Raf1 and H-Ras/RalGDS. Ras is a central switch in …

Significant progress has been achieved in computational methods to treat solvent effects in
recent years. Among various techniques, the continuum solvent approach appears to be …

Implicit solvent models for biomolecular simulations are reviewed and their underlying
statistical mechanical basis is discussed. The fundamental quantity that implicit models seek …

Estimating protein–protein interaction energies is a very challenging task for current
simulation protocols. Here, absolute binding free energies are reported for the complex H …

▪ Abstract It would often be useful in computer simulations to use a simple description of
solvation effects, instead of explicitly representing the individual solvent molecules …

This study compares generalized Born (GB) and Poisson (PB) methods for calculating
electrostatic solvation energies of proteins. A large set of GB and PB implementations from …