The transformational role of GPU computing and deep learning in drug discovery

M Pandey, M Fernandez, F Gentile, O Isayev… - Nature Machine …, 2022 - nature.com
Deep learning has disrupted nearly every field of research, including those of direct
importance to drug discovery, such as medicinal chemistry and pharmacology. This …

Machine learning interatomic potentials and long-range physics

DM Anstine, O Isayev - The Journal of Physical Chemistry A, 2023 - ACS Publications
Advances in machine learned interatomic potentials (MLIPs), such as those using neural
networks, have resulted in short-range models that can infer interaction energies with near …

[HTML][HTML] DeePMD-kit v2: A software package for deep potential models

J Zeng, D Zhang, D Lu, P Mo, Z Li, Y Chen… - The Journal of …, 2023 - pubs.aip.org
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 …

MACE: Higher order equivariant message passing neural networks for fast and accurate force fields

I Batatia, DP Kovacs, G Simm… - Advances in neural …, 2022 - proceedings.neurips.cc
Creating fast and accurate force fields is a long-standing challenge in computational
chemistry and materials science. Recently, Equivariant Message Passing Neural Networks …

Physics-inspired structural representations for molecules and materials

F Musil, A Grisafi, AP Bartók, C Ortner… - Chemical …, 2021 - ACS Publications
The first step in the construction of a regression model or a data-driven analysis, aiming to
predict or elucidate the relationship between the atomic-scale structure of matter and its …

Extending machine learning beyond interatomic potentials for predicting molecular properties

N Fedik, R Zubatyuk, M Kulichenko, N Lubbers… - Nature Reviews …, 2022 - nature.com
Abstract Machine learning (ML) is becoming a method of choice for modelling complex
chemical processes and materials. ML provides a surrogate model trained on a reference …

Choosing the right molecular machine learning potential

M Pinheiro, F Ge, N Ferré, PO Dral, M Barbatti - Chemical Science, 2021 - pubs.rsc.org
Quantum-chemistry simulations based on potential energy surfaces of molecules provide
invaluable insight into the physicochemical processes at the atomistic level and yield such …

The design space of e (3)-equivariant atom-centered interatomic potentials

I Batatia, S Batzner, DP Kovács, A Musaelian… - arxiv preprint arxiv …, 2022 - arxiv.org
The rapid progress of machine learning interatomic potentials over the past couple of years
produced a number of new architectures. Particularly notable among these are the Atomic …

Computational approaches for organic semiconductors: from chemical and physical understanding to predicting new materials

V Bhat, CP Callaway, C Risko - Chemical Reviews, 2023 - ACS Publications
While a complete understanding of organic semiconductor (OSC) design principles remains
elusive, computational methods─ ranging from techniques based in classical and quantum …

Scoring functions for protein-ligand binding affinity prediction using structure-based deep learning: a review

R Meli, GM Morris, PC Biggin - Frontiers in bioinformatics, 2022 - frontiersin.org
The rapid and accurate in silico prediction of protein-ligand binding free energies or binding
affinities has the potential to transform drug discovery. In recent years, there has been a …