Integrating QSAR modelling and deep learning in drug discovery: the emergence of deep QSAR

A Tropsha, O Isayev, A Varnek, G Schneider… - Nature Reviews Drug …, 2024 - nature.com
Quantitative structure–activity relationship (QSAR) modelling, an approach that was
introduced 60 years ago, is widely used in computer-aided drug design. In recent years …

Machine learning-aided generative molecular design

Y Du, AR Jamasb, J Guo, T Fu, C Harris… - Nature Machine …, 2024 - nature.com
Abstract Machine learning has provided a means to accelerate early-stage drug discovery
by combining molecule generation and filtering steps in a single architecture that leverages …

Invalid SMILES are beneficial rather than detrimental to chemical language models

MA Skinnider - Nature Machine Intelligence, 2024 - nature.com
Generative machine learning models have attracted intense interest for their ability to
sample novel molecules with desired chemical or biological properties. Among these …

Pocketflow is a data-and-knowledge-driven structure-based molecular generative model

Y Jiang, G Zhang, J You, H Zhang, R Yao… - Nature Machine …, 2024 - nature.com
Deep learning-based molecular generation has extensive applications in many fields,
particularly drug discovery. However, the majority of current deep generative models are …

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 …

[HTML][HTML] Chemical language models for de novo drug design: Challenges and opportunities

F Grisoni - Current Opinion in Structural Biology, 2023 - Elsevier
Generative deep learning is accelerating de novo drug design, by allowing the generation of
molecules with desired properties on demand. Chemical language models–which generate …

Evaluation guidelines for machine learning tools in the chemical sciences

A Bender, N Schneider, M Segler… - Nature Reviews …, 2022 - nature.com
Abstract Machine learning (ML) promises to tackle the grand challenges in chemistry and
speed up the generation, improvement and/or ordering of research hypotheses. Despite the …

Chemical language modeling with structured state space sequence models

R Özçelik, S de Ruiter, E Criscuolo, F Grisoni - Nature Communications, 2024 - nature.com
Generative deep learning is resha** drug design. Chemical language models (CLMs)–
which generate molecules in the form of molecular strings–bear particular promise for this …

Generative machine learning for de novo drug discovery: A systematic review

DD Martinelli - Computers in Biology and Medicine, 2022 - Elsevier
Recent research on artificial intelligence indicates that machine learning algorithms can
auto-generate novel drug-like molecules. Generative models have revolutionized de novo …

Leveraging molecular structure and bioactivity with chemical language models for de novo drug design

M Moret, I Pachon Angona, L Cotos, S Yan… - Nature …, 2023 - nature.com
Generative chemical language models (CLMs) can be used for de novo molecular structure
generation by learning from a textual representation of molecules. Here, we show that hybrid …