Journal of computer-aided molecular design
Mar 22, 2022
Modern molecular docking comprises the prediction of pose and affinity. Prediction of docking poses is required for affinity prediction when three-dimensional coordinates of the ligand have not been provided. However, a large number of feature engine...
Molecular dynamics (MD) simulations are widely used to obtain the microscopic properties of atomistic systems when the interatomic potential or the coarse-grained potential is known. In many practical situations, however, it is necessary to predict t...
Journal of chemical theory and computation
Feb 24, 2022
We introduce a Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and free energy profiling workflow (GLOW) to predict molecular determinants and map free energy landscapes of biomolecules. All-atom GaMD-enhanced sampling simulations...
Journal of chemical information and modeling
Feb 4, 2022
Fast and accurate assessment of small-molecule dihedral energetics is crucial for molecular design and optimization in medicinal chemistry. Yet, accurate prediction of torsion energy profiles remains challenging as the current molecular mechanics (MM...
Journal of chemical information and modeling
Jan 19, 2022
We present a group contribution method (SoluteGC) and a machine learning model (SoluteML) to predict the Abraham solute parameters, as well as a machine learning model (DirectML) to predict solvation free energy and enthalpy at 298 K. The proposed gr...
Fine materials (FM) from municipal solid waste (MSW) classification require disposal, and pyrolysis is a feasible method for the treatments. Hence, the behavior, kinetics, and products of FM pyrolysis were investigated in this study. A deep learning ...
Total electronic energies and frequencies predicted using the deep learning models ANI-1x and ANI-1ccx are converted to gas-phase formation enthalpies Δ H using an atom equivalent (AE) scheme for a database of CHNO compounds. As expected from the acc...
Journal of computer-aided molecular design
Oct 28, 2021
The advent of computational drug discovery holds the promise of significantly reducing the effort of experimentalists, along with monetary cost. More generally, predicting the binding of small organic molecules to biological macromolecules has far-re...
The journal of physical chemistry letters
Sep 23, 2021
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential. The converg...
Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protei...