The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …

While significant advances have been made in predicting static protein structures, the
inherent dynamics of proteins, modulated by ligands, are crucial for understanding protein …

Energetic local frustration offers a biophysical perspective to interpret the effects of
sequence variability on protein families. Here we present a methodology to analyze local …

Despite the great promise of genetic code expansion technology to modulate structures and
functions of proteins, external addition of ncAAs is required in most cases and it often limits …

Molecular dynamics simulations are an invaluable tool to characterize the dynamic motions
of proteins in atomistic detail. However, the accuracy of models derived from simulations …

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of
coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics …

Bacteriophage T7 gp4 helicase has served as a model system for understanding
mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how …

Bacteria use two-component systems (TCSs) to sense environmental conditions and change
gene expression in response to those conditions. To amplify cellular responses, many …

Heme is an active center in many proteins. Here we explore computationally the role of
heme in protein folding and protein structure. We model heme proteins using a hybrid model …