Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …

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

Scoring functions are essential for modern in silico drug discovery. However, the accurate
prediction of binding affinity by scoring functions remains a challenging task. The …

We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and
free energy methods in Amber18. Of particular interest is the development of alchemical free …

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

Quantitative prediction of physical properties of liquids is important for many applications.
Computational methods based on either explicit or implicit solvent models can be used to …

Classical atomistic simulations, also known as molecular mechanics simulations, use simple
potential-energy functions to model molecular systems at the atomic level. In this …

Accurate computational prediction of protein structure represents a longstanding challenge
in molecular biology and structure‐based drug design. Although homology modeling …

Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the
structure, function, and motion of proteins for students, faculty, and researchers at all levels …

Constant pH molecular dynamics (MD) simulations sample protonation states on the fly
according to the conformational environment and user specified pH conditions; however, the …