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 …

3d infomax improves gnns for molecular property prediction

H Stärk, D Beaini, G Corso, P Tossou… - International …, 2022 - proceedings.mlr.press
Molecular property prediction is one of the fastest-growing applications of deep learning with
critical real-world impacts. Although the 3D molecular graph structure is necessary for …

[HTML][HTML] 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 …

[HTML][HTML] Leveraging large language models for predictive chemistry

KM Jablonka, P Schwaller… - Nature Machine …, 2024 - nature.com
Abstract Machine learning has transformed many fields and has recently found applications
in chemistry and materials science. The small datasets commonly found in chemistry …

[HTML][HTML] Prospective de novo drug design with deep interactome learning

K Atz, L Cotos, C Isert, M Håkansson, D Focht… - Nature …, 2024 - nature.com
De novo drug design aims to generate molecules from scratch that possess specific
chemical and pharmacological properties. We present a computational approach utilizing …

[HTML][HTML] Past, present, and future perspectives on computer-aided drug design methodologies

D Bassani, S Moro - Molecules, 2023 - mdpi.com
The application of computational approaches in drug discovery has been consolidated in
the last decades. These families of techniques are usually grouped under the common …

Is GPT-3 all you need for low-data discovery in chemistry?

Machine learning has revolutionized many fields and has recently found applications in
chemistry and materials science. The small datasets commonly found in chemistry lead to …

[HTML][HTML] Enabling late-stage drug diversification by high-throughput experimentation with geometric deep learning

DF Nippa, K Atz, R Hohler, AT Müller, A Marx… - Nature Chemistry, 2024 - nature.com
Late-stage functionalization is an economical approach to optimize the properties of drug
candidates. However, the chemical complexity of drug molecules often makes late-stage …

[HTML][HTML] Δ-Quantum machine-learning for medicinal chemistry

K Atz, C Isert, MNA Böcker, J Jiménez-Luna… - Physical Chemistry …, 2022 - pubs.rsc.org
Many molecular design tasks benefit from fast and accurate calculations of quantum-
mechanical (QM) properties. However, the computational cost of QM methods applied to …