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Machine learning of reactive potentials
In the past two decades, machine learning potentials (MLPs) have driven significant
developments in chemical, biological, and material sciences. The construction and training …
developments in chemical, biological, and material sciences. The construction and training …
Modern alchemical free energy methods for drug discovery explained
DM York - ACS Physical Chemistry Au, 2023 - ACS Publications
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 …
free energy methods and their role in drug discovery as well as highlights select emerging …
Hybrid quantum mechanical/molecular mechanical methods for studying energy transduction in biomolecular machines
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become
indispensable tools for the study of biomolecules. In this article, we briefly review the basic …
indispensable tools for the study of biomolecules. In this article, we briefly review the basic …
Condensed matter systems exposed to radiation: multiscale theory, simulations, and experiment
This roadmap reviews the new, highly interdisciplinary research field studying the behavior
of condensed matter systems exposed to radiation. The Review highlights several recent …
of condensed matter systems exposed to radiation. The Review highlights several recent …
QDπ: A quantum deep potential interaction model for drug discovery
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 …
and O atoms. The QDπ model is in the form of a quantum mechanical/machine learning …
Combined QM/MM, machine learning path integral approach to compute free energy profiles and kinetic isotope effects in RNA cleavage reactions
We present a fast, accurate, and robust approach for determination of free energy profiles
and kinetic isotope effects for RNA 2′-O-transphosphorylation reactions with inclusion of …
and kinetic isotope effects for RNA 2′-O-transphosphorylation reactions with inclusion of …
Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states
Modern semiempirical electronic structure methods have considerable promise in drug
discovery as universal “force fields” that can reliably model biological and drug-like …
discovery as universal “force fields” that can reliably model biological and drug-like …
How Accurate Are QM/MM Models?
Despite the success and widespread use of QM/MM methods in modeling (bio) chemically
important processes, their accuracy is still not well understood. A key reason is because …
important processes, their accuracy is still not well understood. A key reason is because …
Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates
Fast and accurate prediction of solvent effects on reaction rates are crucial for kinetic
modeling, chemical process design, and high-throughput solvent screening. Despite the …
modeling, chemical process design, and high-throughput solvent screening. Despite the …
Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation
Free energy simulations that employ combined quantum mechanical and molecular
mechanical (QM/MM) potentials at ab initio QM (AI) levels are computationally highly …
mechanical (QM/MM) potentials at ab initio QM (AI) levels are computationally highly …