Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

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

A unified coarse-grained model of three major classes of biological molecules—proteins,
nucleic acids, and polysaccharides—has been developed. It is based on the observations …

Proteins provide much of the scaffolding for life, as well as undertaking a variety of essential
catalytic reactions. These characteristic functions have led us to presuppose that proteins …

Interplay between cellular membranes and their peripheral proteins drives many processes
in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular …

The precise regulation of AMPA receptor (AMPAR) trafficking in neurons is crucial for
excitatory neurotransmission, synaptic plasticity and the consequent formation and …

The PDZ family is comprised of small modular domains that play critical roles in the allosteric
modulation of many cellular signaling processes by binding to the C‐terminal tail of different …

We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of
protein structure and dynamics, which is being developed in our laboratory over the last …

Abstract Graphical Processor Units (GPUs) are nowadays widely used in all-atom molecular
simulations because of the advantage of efficient partitioning of atom pairs between the …

The unfolded state of proteins presents many challenges to elucidate the structural basis for
biological function. This state is characterized by a large degree of structural heterogeneity …