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 …

Deep learning methods for molecular representation and property prediction

Z Li, M Jiang, S Wang, S Zhang - Drug Discovery Today, 2022 - Elsevier
Highlights•The deep learning method could effectively represent the molecular structure and
predict molecular property through diversified models.•One, two, and three-dimensional …

Machine learning enables interpretable discovery of innovative polymers for gas separation membranes

J Yang, L Tao, J He, JR McCutcheon, Y Li - Science Advances, 2022 - science.org
Polymer membranes perform innumerable separations with far-reaching environmental
implications. Despite decades of research, design of new membrane materials remains a …

Artificial intelligence for natural product drug discovery

MW Mullowney, KR Duncan, SS Elsayed… - Nature Reviews Drug …, 2023 - nature.com
Developments in computational omics technologies have provided new means to access
the hidden diversity of natural products, unearthing new potential for drug discovery. In …

Accelerated rational PROTAC design via deep learning and molecular simulations

S Zheng, Y Tan, Z Wang, C Li, Z Zhang… - Nature Machine …, 2022 - nature.com
Proteolysis-targeting chimeras (PROTACs) have emerged as effective tools to selectively
degrade disease-related proteins by using the ubiquitin-proteasome system. Developing …

Deep learning in virtual screening: recent applications and developments

TB Kimber, Y Chen, A Volkamer - International journal of molecular …, 2021 - mdpi.com
Drug discovery is a cost and time-intensive process that is often assisted by computational
methods, such as virtual screening, to speed up and guide the design of new compounds …

Model agnostic generation of counterfactual explanations for molecules

GP Wellawatte, A Seshadri, AD White - Chemical science, 2022 - pubs.rsc.org
An outstanding challenge in deep learning in chemistry is its lack of interpretability. The
inability of explaining why a neural network makes a prediction is a major barrier to …

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 …

Explainable, domain-adaptive, and federated artificial intelligence in medicine

A Chaddad, Q Lu, J Li, Y Katib, R Kateb… - IEEE/CAA Journal of …, 2023 - ieeexplore.ieee.org
Artificial intelligence (AI) continues to transform data analysis in many domains. Progress in
each domain is driven by a growing body of annotated data, increased computational …

Explainable machine learning for property predictions in compound optimization: miniperspective

R Rodríguez-Pérez, J Bajorath - Journal of medicinal chemistry, 2021 - ACS Publications
The prediction of compound properties from chemical structure is a main task for machine
learning (ML) in medicinal chemistry. ML is often applied to large data sets in applications …