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 …

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 ability to predict transport properties (eg, diffusivity, viscosity, and conductivity) is one of
the primary benefits of molecular simulation. Although most studies focus on the accuracy of …

Abstract 3Drefine is an interactive web server for consistent and computationally efficient
protein structure refinement with the capability to perform web-based statistical and visual …

Successive parameterizations of the GROMOS force field have been used successfully to
simulate biomolecular systems over a long period of time. The continuing expansion of …

Pseudomonas aeruginosa, the principal pathogen of cystic fibrosis patients, forms antibiotic‐
resistant biofilms promoting chronic colonization of the airways. The extracellular (EPS) …

Molecular dynamics simulations of the protein chymotrypsin inhibitor 2 in 8 M urea at 60° C
were undertaken to investigate the molecular basis of chemical denaturation. The protein …

A grand challenge in the field of structural biology is to design and engineer proteins that
exhibit targeted functions. Although much success on this front has been achieved, design …

The ability to separate correct models of protein structures from less correct models is of the
greatest importance for protein structure prediction methods. Several studies have examined …

Integrative structural biology attempts to model the structures of protein complexes that are
challenging or intractable by classical structural methods (due to size, dynamics, or …