Deep learning in chemistry

AC Mater, ML Coote - Journal of chemical information and …, 2019 - ACS Publications
Machine learning enables computers to address problems by learning from data. Deep
learning is a type of machine learning that uses a hierarchical recombination of features to …

Structure-based virtual screening for ligands of G protein–coupled receptors: what can molecular docking do for you?

F Ballante, AJ Kooistra, S Kampen, C de Graaf… - Pharmacological …, 2021 - ASPET
G protein–coupled receptors (GPCRs) constitute the largest family of membrane proteins in
the human genome and are important therapeutic targets. During the last decade, the …

Pushing the boundaries of molecular representation for drug discovery with the graph attention mechanism

Z Xiong, D Wang, X Liu, F Zhong, X Wan… - Journal of medicinal …, 2019 - ACS Publications
Hunting for chemicals with favorable pharmacological, toxicological, and pharmacokinetic
properties remains a formidable challenge for drug discovery. Deep learning provides us …

Smiles-bert: large scale unsupervised pre-training for molecular property prediction

S Wang, Y Guo, Y Wang, H Sun, J Huang - Proceedings of the 10th ACM …, 2019 - dl.acm.org
With the rapid progress of AI in both academia and industry, Deep Learning has been widely
introduced into various areas in drug discovery to accelerate its pace and cut R&D costs …

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

AJ Williams, CM Grulke, J Edwards… - Journal of …, 2017 - Springer
Despite an abundance of online databases providing access to chemical data, there is
increasing demand for high-quality, structure-curated, open data to meet the various needs …

MoleculeNet: a benchmark for molecular machine learning

Z Wu, B Ramsundar, EN Feinberg, J Gomes… - Chemical …, 2018 - pubs.rsc.org
Molecular machine learning has been maturing rapidly over the last few years. Improved
methods and the presence of larger datasets have enabled machine learning algorithms to …

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 …

Biological network analysis with deep learning

G Muzio, L O'Bray, K Borgwardt - Briefings in bioinformatics, 2021 - academic.oup.com
Recent advancements in experimental high-throughput technologies have expanded the
availability and quantity of molecular data in biology. Given the importance of interactions in …

Deep learning for computational chemistry

GB Goh, NO Hodas, A Vishnu - Journal of computational …, 2017 - Wiley Online Library
The rise and fall of artificial neural networks is well documented in the scientific literature of
both computer science and computational chemistry. Yet almost two decades later, we are …

Molecular graph convolutions: moving beyond fingerprints

S Kearnes, K McCloskey, M Berndl, V Pande… - Journal of computer …, 2016 - Springer
Molecular “fingerprints” encoding structural information are the workhorse of
cheminformatics and machine learning in drug discovery applications. However, fingerprint …