Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

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

We developed a Python package, ProDy, for structure-based analysis of protein dynamics.
ProDy allows for quantitative characterization of structural variations in heterogeneous …

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 …

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

Nitric oxide (NO) regulates diverse cellular signaling through S-nitrosylation of specific Cys
residues of target proteins. The intracellular level of S-nitrosoglutathione (GSNO), a major …

Background Popular bioinformatics approaches for studying protein functional dynamics
include comparisons of crystallographic structures, molecular dynamics simulations and …

Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has
proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable …

Correlations between sequence evolution and structural dynamics are of utmost importance
in understanding the molecular mechanisms of function and their evolution. We have …