[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 …

[HTML][HTML] Electrostatic aspects of protein–protein interactions

FB Sheinerman, R Norel, B Honig - Current opinion in structural biology, 2000 - Elsevier
Structural and mutational analyses reveal a central role for electrostatic interactions in
protein–protein association. Experiment and theory both demonstrate that clusters of …

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 …

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent …

W Wang, O Donini, CM Reyes… - Annual review of …, 2001 - annualreviews.org
▪ Abstract Computer modeling has been developed and widely applied in studying
molecules of biological interest. The force field is the cornerstone of computer simulations …

Theoretical and computational models of biological ion channels

B Roux, T Allen, S Berneche, W Im - Quarterly reviews of biophysics, 2004 - cambridge.org
1. Introduction 172. Dynamics of many-body systems 192.1 Effective dynamics of reduced
systems 212.2 The constraint of thermodynamic equilibrium 242.3 Mean-field theories 253 …

[图书][B] Computational biochemistry and biophysics

OM Becker, AD MacKerell, B Roux, M Watanabe - 2001 - api.taylorfrancis.com
The first dynamical simulation of a protein based on a detailed atomic model was reported in
1977. Since then, the uses of various theoretical and computational approaches have …

Structure and interactions of biological helices

AA Kornyshev, DJ Lee, S Leikin, A Wynveen - Reviews of Modern Physics, 2007 - APS
Helices are essential building blocks of living organisms, be they molecular fragments of
proteins (α-helices), macromolecules (DNA and collagen), or multimolecular assemblies …

Protonation and pK changes in protein–ligand binding

AV Onufriev, E Alexov - Quarterly reviews of biophysics, 2013 - cambridge.org
Formation of protein–ligand complexes causes various changes in both the receptor and the
ligand. This review focuses on changes in pK and protonation states of ionizable groups that …

Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components

PL Privalov, AI Dragan… - Nucleic acids …, 2011 - academic.oup.com
We discuss the effectiveness of existing methods for understanding the forces driving the
formation of specific protein–DNA complexes. Theoretical approaches using the Poisson …

Poisson–Boltzmann methods for biomolecular electrostatics

NA Baker - Methods in enzymology, 2004 - Elsevier
Publisher Summary This chapter presents Poisson-Boltzmann (PB) methods for
biomolecular electrostatics. The understanding of electrostatic properties is a basic aspect of …