Knowledge of protein structure is paramount to the understanding of biological function,
developing new therapeutics, and making detailed mechanistic hypotheses. Therefore …

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

Proteins are fascinating supramolecular structures, which are able to recognize ligands
transforming binding information into chemical signals. They can transfer information across …

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 …

Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …

The generalized Born (GB) model is one of the fastest implicit solvent models, and it has
become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with …

ATP binding cassette (ABC) transporters play critical roles in maintaining sterol balance in
higher eukaryotes. The ABCG5/ABCG8 heterodimer (G5G8) mediates excretion of neutral …

Obesity increases the risk for a number of diseases including cardiovascular diseases and
type 2 diabetes. Excess saturated fatty acids (SFAs) in obesity play a significant role in …

Adequate sampling of conformation space remains challenging in atomistic simulations,
especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up …

We propose a new approach for force field optimizations which aims at reproducing
dynamics characteristics using biomolecular MD simulations, in addition to improved …