This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …

Rigorous physics-based methods to calculate binding free energies of protein–ligand
complexes have become a valued component of structure-based drug design. Relative and …

AmberTools | Journal of Chemical Information and Modeling Recently Viewedclose modal ACS
ACS Publications C&EN CAS Find my institution Log In ACS Publications. Most Trusted. Most …

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics
simulations using machine learning potentials known as Deep Potential (DP) models. This …

We present software infrastructure for the design and testing of new quantum
mechanical/molecular mechanical and machine-learning potential (QM/MM− ΔMLP) force …

Introduction For rational drug design, it is crucial to understand the receptor-drug binding
processes and mechanisms. A new era for the use of computer simulations in predicting …

We report an automated workflow for production free-energy simulation setup and analysis
(ProFESSA) using the GPU-accelerated AMBER free-energy engine with enhanced …

In drug discovery, the in silico prediction of binding affinity is one of the major means to
prioritize compounds for synthesis. Alchemical relative binding free energy (RBFE) …

An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate
importance sampling in free energy simulations. The method achieves enhanced sampling …

A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from
exogenous O 6-methylguanine (O 6mG) to a target adenine N1, and recently, high …