Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …

Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

We propose and discuss an efficient scheme for the in silico sampling for parts of the
molecular chemical space by semiempirical tight-binding methods combined with a meta …

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 …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

P450 TleB catalyzes the oxidative cyclization of the dipeptide N-methylvalyl-tryptophanol
into indolactam V through selective intramolecular C–H bond amination at the indole C4 …

Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and
SW2, in K-Ras, which is considered as an important target of anticancer drug design. To …

Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and
play an important role in cellular signaling. However, it is challenging to simulate both …