Molecular dynamics (MD) allows the study of biological and chemical systems at the
atomistic level on timescales from femtoseconds to milliseconds. It complements experiment …

Computer-aided drug design (CADD) is an emerging field that has drawn a lot of interest
because of its potential to expedite and lower the cost of the drug development process …

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force
field is required. The Amber ff99SB force field improved protein secondary structure balance …

Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …

We present parmbsc1, a force field for DNA atomistic simulation, which has been
parameterized from high-level quantum mechanical data and tested for nearly 100 systems …

As part of our ongoing efforts to support diverse force fields and simulation programs in
CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber …

Molecular dynamics simulations capture the behavior of biological macromolecules in full
atomic detail, but their computational demands, combined with the challenge of …

S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation
of bacterial gene expression at the level of transcription attenuation or translation inhibition …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Z-DNA duplexes are a particularly complicated test case for current force fields. We
performed a set of explicit solvent molecular dynamics (MD) simulations with various …