The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven
to be an effective means of capturing the functionally important long-time and large-length …

A novel family of 2Fe–2S proteins, the NEET family, was discovered during the last decade
in numerous organisms, including archea, bacteria, algae, plant and human; suggesting an …

We develop a procedure to characterize the association of protein structures into
homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) …

The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that
instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this …

Protein evolution is guided by structural, functional, and dynamical constraints ensuring
organismal viability. Pseudogenes are genomic sequences identified in many eukaryotes …

Advances in personalized medicine and protein engineering require accurately predicting
outcomes of amino acid substitutions. Many algorithms correctly predict that evolutionarily …

Hsp70s are a class of ubiquitous and highly conserved molecular chaperones playing a
central role in the regulation of proteostasis in the cell. Hsp70s assist a myriad of cellular …

We introduce a model of amino acid sequence evolution that accounts for the statistical
behavior of real sequences induced by epistatic interactions. We base the model dynamics …