The term B-factor, sometimes called the Debye–Waller factor, temperature factor, or atomic
displacement parameter, is used in protein crystallography to describe the attenuation of X …

A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …

Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales
are critical for understanding macromolecular functioning. Coarse-grained representations …

In this study, we used an integrative computational approach to examine molecular
mechanisms and determine functional signatures underlying the role of functional residues …

Abstract Motivation: The Anisotropic Network Model (ANM) is a simple yet powerful model
for normal mode analysis of proteins. Despite its broad use for exploring biomolecular …

For simulating proteins at work in millisecond time scale or longer, we develop a coarse-
grained (CG) molecular dynamics (MD) method and software, CafeMol. At the resolution of …

Recently, we saw a dramatic increase in the number of researches that rely on coarse-
grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently …

The anisotropic network model (ANM) is one of the simplest yet powerful tools for exploring
protein dynamics. Its main utility is to predict and visualize the collective motions of large …

Elastic network models (ENMs) are entropic models that have demonstrated in many
previous studies their abilities to capture overall the important internal motions, with …

Allostery describes altered protein function at one site due to a perturbation at another site.
One mechanism of allostery involves correlated motions, which can occur even in the …