Water is an essential participant in the stability, structure, dynamics, and function of proteins
and other biomolecules. Thermodynamically, changes in the aqueous environment affect …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

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) simulation is a valuable tool for characterizing the structural
dynamics of folded proteins and should be similarly applicable to disordered proteins and …

We present an implementation of generalized Born implicit solvent all-atom classical
molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA …

The chemical composition of small organic molecules is often very similar to amino acid side
chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular …

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and
interactions of biological macromolecules in full atomic detail. The accuracy of such …

Since Anfinsen demonstrated that the information encoded in a protein's amino acid
sequence determines its structure in 1973, solving the protein structure prediction problem …