Experimental studies of protein folding are hampered by the fact that only low-resolution
structural data can be obtained with sufficient temporal resolution. Molecular dynamics …

… We begin with the usage of GPUs to place ions around a solvated system and continue
with the calculation of time-averaged Coulomb potentials in the vicinity of a simulated system. …

This work presents an all-atom molecular dynamics simulation of a complete virus, the satellite
tobacco mosaic virus. Simulations with up to 1 million atoms for over 50 ns demonstrate …

The COFACTOR web server is a unified platform for structure-based multiple-level protein
function predictions. By structurally threading low-resolution structural models through the …

… We are grateful to members of the Freddolino laboratory for many helpful discussions,
and also to the generations of scientists who have contributed to our tremendous body of …

All-atom molecular dynamics (MD) simulations of protein folding allow analysis of the folding
process at an unprecedented level of detail. Unfortunately, such simulations have not yet …

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global,
community-driven effort to evaluate and improve the computational annotation of protein …

… At present, MD is the only methodology that can provide realistic images of microscopic
events taking place inside the nanosensor. Atom by atom, we build microscopic models of the …

We report a study of the structural dynamics of viral capsids, simulated on a microsecond
timescale, by employing a coarse-graining molecular dynamics method. The method was …

A coarse-grained model for molecular dynamics simulations is extended from lipids to proteins.
In the framework of such models pioneered by Klein, atoms are described group-wise by …