Structure-based drug design with geometric deep learning

C Isert, K Atz, G Schneider - Current Opinion in Structural Biology, 2023‏ - Elsevier
Abstract Structure-based drug design uses three-dimensional geometric information of
macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric …

Machine learning force fields

OT Unke, S Chmiela, HE Sauceda… - Chemical …, 2021‏ - ACS Publications
In recent years, the use of machine learning (ML) in computational chemistry has enabled
numerous advances previously out of reach due to the computational complexity of …

Geometric latent diffusion models for 3d molecule generation

M Xu, AS Powers, RO Dror, S Ermon… - International …, 2023‏ - proceedings.mlr.press
Generative models, especially diffusion models (DMs), have achieved promising results for
generating feature-rich geometries and advancing foundational science problems such as …

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 …

Learning local equivariant representations for large-scale atomistic dynamics

A Musaelian, S Batzner, A Johansson, L Sun… - Nature …, 2023‏ - nature.com
A simultaneously accurate and computationally efficient parametrization of the potential
energy surface of molecules and materials is a long-standing goal in the natural sciences …

Pure transformers are powerful graph learners

J Kim, D Nguyen, S Min, S Cho… - Advances in Neural …, 2022‏ - proceedings.neurips.cc
We show that standard Transformers without graph-specific modifications can lead to
promising results in graph learning both in theory and practice. Given a graph, we simply …

Geodiff: A geometric diffusion model for molecular conformation generation

M Xu, L Yu, Y Song, C Shi, S Ermon, J Tang - arxiv preprint arxiv …, 2022‏ - arxiv.org
Predicting molecular conformations from molecular graphs is a fundamental problem in
cheminformatics and drug discovery. Recently, significant progress has been achieved with …

Equiformerv2: Improved equivariant transformer for scaling to higher-degree representations

YL Liao, B Wood, A Das, T Smidt - arxiv preprint arxiv:2306.12059, 2023‏ - arxiv.org
Equivariant Transformers such as Equiformer have demonstrated the efficacy of applying
Transformers to the domain of 3D atomistic systems. However, they are limited to small …

Equiformer: Equivariant graph attention transformer for 3d atomistic graphs

YL Liao, T Smidt - arxiv preprint arxiv:2206.11990, 2022‏ - arxiv.org
Despite their widespread success in various domains, Transformer networks have yet to
perform well across datasets in the domain of 3D atomistic graphs such as molecules even …

e3nn: Euclidean neural networks

M Geiger, T Smidt - arxiv preprint arxiv:2207.09453, 2022‏ - arxiv.org
We present e3nn, a generalized framework for creating E (3) equivariant trainable functions,
also known as Euclidean neural networks. e3nn naturally operates on geometry and …