Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

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 …

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and
dynamics. Major functionality includes biomolecular database searching and retrieval …

Phaser is a program for phasing macromolecular crystal structures by both molecular
replacement and experimental phasing methods. The novel phasing algorithms …

Structure-based and physics-based coarse-grained molecular force fields have become
attractive approaches to gain mechanistic insight into the function of large biomolecular …

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie
their biological functions. Recent studies indicate that these dynamic properties are …

A normal mode analysis of 20 proteins inopen'orclosed'forms was performed using simple
potential and protein models. The quality of the results was found to depend upon the form …

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a
given macromolecule. It has been shown recently that half of the known protein movements …

The realization that experimentally observed functional motions of proteins can be predicted
by coarse-grained normal mode analysis has renewed interest in applications to structural …