Water dynamics in the hydration shells of biomolecules

D Laage, T Elsaesser, JT Hynes - Chemical Reviews, 2017 - ACS Publications
The structure and function of biomolecules are strongly influenced by their hydration shells.
Structural fluctuations and molecular excitations of hydrating water molecules cover a broad …

Classical electrostatics in biology and chemistry

B Honig, A Nicholls - Science, 1995 - science.org
A major revival in the use of classical electrostatics as an approach to the study of charged
and polar molecules in aqueous solution has been made possible through the development …

The role of DNA shape in protein–DNA recognition

R Rohs, SM West, A Sosinsky, P Liu, RS Mann… - Nature, 2009 - nature.com
The recognition of specific DNA sequences by proteins is thought to depend on two types of
mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily …

Origins of specificity in protein-DNA recognition

R Rohs, X **, SM West, R Joshi… - Annual review of …, 2010 - annualreviews.org
Specific interactions between proteins and DNA are fundamental to many biological
processes. In this review, we provide a revised view of protein-DNA interactions that …

[PDF][PDF] Interactions in macromolecules: theory and applications

KA Sharp, B Honi - Annu. Rev. Biophys. Biophys. Chem, 1990 - researchgate.net
302 SHARP & HONIG who then jumped in unison to the great amusement of the onlookers
(67a). The point of the story, in the context of the article,. was that" electrostatics was not …

Understanding nucleic acid–ion interactions

J Lipfert, S Doniach, R Das… - Annual review of …, 2014 - annualreviews.org
Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the
folding and dynamics of RNA and DNA and their complexes with proteins and with each …

A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation

A Nicholls, B Honig - Journal of computational chemistry, 1991 - Wiley Online Library
An efficient algorithm is presented for the numerical solution of the Poisson–Boltzmann
equation by the finite difference method of successive over‐relaxation. Improvements …

Electrostatics in biomolecular structure and dynamics

ME Davis, JA McCammon - Chemical Reviews, 1990 - ACS Publications
Electromagnetism is the force of chemistry. Combined with the consequences of
quantumand statistical mechanics, electromagnetic forces maintain the structure and drive …

Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation

KA Sharp, B Honig - Journal of Physical Chemistry, 1990 - ACS Publications
The Poisson-Boltzmann (PB) equation has long been used for modeling the electrostatic
properties of membranes, colloids, polyelectrolytes and macromolecules. Analytical …

Theoretical methods for the description of the solvent effect in biomolecular systems

M Orozco, FJ Luque - Chemical Reviews, 2000 - ACS Publications
The environment plays a key role in the determination of the properties and reactivity of
substances in condensed phases. The complexity of chemical phenomena in solution has …