Machine learning models are poised to make a transformative impact on chemical sciences
by dramatically accelerating computational algorithms and amplifying insights available from …

Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …

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 …

Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful
computational method for fundamental research in science branches such as biology …

Molecular docking is an established in silico structure-based method widely used in drug
discovery. Docking enables the identification of novel compounds of therapeutic interest …

TeraChem was born in 2008 with the goal of providing fast on‐the‐fly electronic structure
calculations to facilitate ab initio molecular dynamics studies of large biochemical systems …

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 …

Structure-based virtual screening relies on classical scoring functions that often fail to
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …

Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a
potentially useful tool for accelerating molecular dynamics (MD) simulations. By …

Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …