Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …

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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 …

We present an alchemical enhanced sampling (ACES) method implemented in the GPU-
accelerated AMBER free energy MD engine. The methods hinges on the creation of an …

We develop a framework for the design of optimized alchemical transformation pathways in
free energy simulations using nonlinear mixing and a new functional form for so-called …

Computational techniques can speed up the identification of hits and accelerate the
development of candidate molecules for drug discovery. Among techniques for predicting …

We report QDπ-v1. 0 for modeling the internal energy of drug molecules containing H, C, N,
and O atoms. The QDπ model is in the form of a quantum mechanical/machine learning …

In the simulation of molecular systems, the underlying force field (FF) model plays an
extremely important role in determining the reliability of the simulation. However, the quality …

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

Membrane proteins have diverse functions within cells and are well-established drug
targets. The advances in membrane protein structural biology have revealed drug and lipid …