Generalized Born implicit solvent models for biomolecules

AV Onufriev, DA Case - Annual review of biophysics, 2019 - annualreviews.org
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 …

Quantum mechanical continuum solvation models

J Tomasi, B Mennucci, R Cammi - Chemical reviews, 2005 - ACS Publications
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 …

The Amber biomolecular simulation programs

DA Case, TE Cheatham III, T Darden… - Journal of …, 2005 - Wiley Online Library
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 …

Exploring protein native states and large‐scale conformational changes with a modified generalized born model

A Onufriev, D Bashford, DA Case - Proteins: Structure, Function …, 2004 - Wiley Online Library
Implicit solvation models provide, for many applications, a reasonably accurate and
computationally effective way to describe the electrostatics of aqueous solvation. Here, a …

Force fields for protein simulations

JW Ponder, DA Case - Advances in protein chemistry, 2003 - Elsevier
Publisher Summary The chapter focuses on a general description of the force fields that are
most commonly used at present, and it gives an indication of the directions of current …

[PDF][PDF] Implicit solvation models: equilibria, structure, spectra, and dynamics

CJ Cramer, DG Truhlar - Chemical Reviews, 1999 - Citeseer
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 …

Modification of the generalized Born model suitable for macromolecules

A Onufriev, D Bashford, DA Case - The Journal of Physical …, 2000 - ACS Publications
The analytic generalized Born approximation is an efficient electrostatic model that
describes molecules in solution. Here it is modified to permit a more accurate description of …

A view of the hydrophobic effect

NT Southall, KA Dill, ADJ Haymet - The Journal of Physical …, 2002 - ACS Publications
Oil and water do not mix. The disaffinity of oil for water, with its unusual temperature
dependence, is called the hydrophobic effect. It is important to understand the factors …

Implicit solvent models

B Roux, T Simonson - Biophysical chemistry, 1999 - Elsevier
Implicit solvent models for biomolecular simulations are reviewed and their underlying
statistical mechanical basis is discussed. The fundamental quantity that implicit models seek …

Calculation of protein-ligand binding affinities

MK Gilson, HX Zhou - Annu. Rev. Biophys. Biomol. Struct., 2007 - annualreviews.org
Accurate methods of computing the affinity of a small molecule with a protein are needed to
speed the discovery of new medications and biological probes. This paper reviews physics …