Ab initio machine learning in chemical compound space

B Huang, OA Von Lilienfeld - Chemical reviews, 2021 - ACS Publications
Chemical compound space (CCS), the set of all theoretically conceivable combinations of
chemical elements and (meta-) stable geometries that make up matter, is colossal. The first …

Data generation for machine learning interatomic potentials and beyond

M Kulichenko, B Nebgen, N Lubbers, JS Smith… - Chemical …, 2024 - ACS Publications
The field of data-driven chemistry is undergoing an evolution, driven by innovations in
machine learning models for predicting molecular properties and behavior. Recent strides in …

E (n) equivariant graph neural networks

VG Satorras, E Hoogeboom… - … conference on machine …, 2021 - proceedings.mlr.press
This paper introduces a new model to learn graph neural networks equivariant to rotations,
translations, reflections and permutations called E (n)-Equivariant Graph Neural Networks …

Pre-training via denoising for molecular property prediction

S Zaidi, M Schaarschmidt, J Martens, H Kim… - arXiv preprint arXiv …, 2022 - arxiv.org
Many important problems involving molecular property prediction from 3D structures have
limited data, posing a generalization challenge for neural networks. In this paper, we …

MACE-OFF23: Transferable machine learning force fields for organic molecules

DP Kovács, JH Moore, NJ Browning, I Batatia… - arXiv preprint arXiv …, 2023 - arxiv.org
Classical empirical force fields have dominated biomolecular simulation for over 50 years.
Although widely used in drug discovery, crystal structure prediction, and biomolecular …

Spice, a dataset of drug-like molecules and peptides for training machine learning potentials

P Eastman, PK Behara, DL Dotson, R Galvelis, JE Herr… - Scientific Data, 2023 - nature.com
Abstract Machine learning potentials are an important tool for molecular simulation, but their
development is held back by a shortage of high quality datasets to train them on. We …

GemNet-OC: developing graph neural networks for large and diverse molecular simulation datasets

J Gasteiger, M Shuaibi, A Sriram, S Günnemann… - arXiv preprint arXiv …, 2022 - arxiv.org
Recent years have seen the advent of molecular simulation datasets that are orders of
magnitude larger and more diverse. These new datasets differ substantially in four aspects …

A quantum chemical interaction energy dataset for accurately modeling protein-ligand interactions

SA Spronk, ZL Glick, DP Metcalf, CD Sherrill… - Scientific Data, 2023 - nature.com
Fast and accurate calculation of intermolecular interaction energies is desirable for
understanding many chemical and biological processes, including the binding of small …

Machine-learned molecular mechanics force fields from large-scale quantum chemical data

K Takaba, AJ Friedman, CE Cavender, PK Behara… - Chemical …, 2024 - pubs.rsc.org
The development of reliable and extensible molecular mechanics (MM) force fields—fast,
empirical models characterizing the potential energy surface of molecular systems—is …

Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields

PK Behara, H Jang, JT Horton, T Gokey… - The Journal of …, 2024 - ACS Publications
A wide range of density functional methods and basis sets are available to derive the
electronic structure and properties of molecules. Quantum mechanical calculations are too …