Geometric deep learning on molecular representations

K Atz, F Grisoni, G Schneider - Nature Machine Intelligence, 2021 - nature.com
Geometric deep learning (GDL) is based on neural network architectures that incorporate
and process symmetry information. GDL bears promise for molecular modelling applications …

[HTML][HTML] 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 …

Geometric deep learning for drug discovery

M Liu, C Li, R Chen, D Cao, X Zeng - Expert Systems with Applications, 2023 - Elsevier
Drug discovery is a time-consuming and expensive process. With the development of
Artificial Intelligence (AI) techniques, molecular Geometric Deep Learning (GDL) has …

[HTML][HTML] Enhancing geometric representations for molecules with equivariant vector-scalar interactive message passing

Y Wang, T Wang, S Li, X He, M Li, Z Wang… - Nature …, 2024 - nature.com
Geometric deep learning has been revolutionizing the molecular modeling field. Despite the
state-of-the-art neural network models are approaching ab initio accuracy for molecular …

A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems

A Duval, SV Mathis, CK Joshi, V Schmidt… - arXiv preprint arXiv …, 2023 - arxiv.org
Recent advances in computational modelling of atomic systems, spanning molecules,
proteins, and materials, represent them as geometric graphs with atoms embedded as …

Symmetry-informed geometric representation for molecules, proteins, and crystalline materials

S Liu, Y Li, Z Li, Z Zheng, C Duan… - Advances in neural …, 2024 - proceedings.neurips.cc
Artificial intelligence for scientific discovery has recently generated significant interest within
the machine learning and scientific communities, particularly in the domains of chemistry …

Geometric deep learning for structure-based ligand design

AS Powers, HH Yu, P Suriana, RV Koodli… - ACS Central …, 2023 - ACS Publications
A pervasive challenge in drug design is determining how to expand a ligand─ a small
molecule that binds to a target biomolecule─ in order to improve various properties of the …

DG‐GL: Differential geometry‐based geometric learning of molecular datasets

DD Nguyen, GW Wei - International journal for numerical …, 2019 - Wiley Online Library
Motivation: Despite its great success in various physical modeling, differential geometry
(DG) has rarely been devised as a versatile tool for analyzing large, diverse, and complex …

Enhanced Deep‐Learning Prediction of Molecular Properties via Augmentation of Bond Topology

H Cho, IS Choi - ChemMedChem, 2019 - Wiley Online Library
Deep learning has made great strides in tackling chemical problems, but still lacks full‐
fledged representations for three‐dimensional (3D) molecular structures for its inner …

A review of mathematical representations of biomolecular data

DD Nguyen, Z Cang, GW Wei - Physical Chemistry Chemical Physics, 2020 - pubs.rsc.org
Recently, machine learning (ML) has established itself in various worldwide benchmarking
competitions in computational biology, including Critical Assessment of Structure Prediction …