AI in Drug Discovery - A Highly Opinionated Literature Review (Part III)


Following up on Part I and Part II, the third post in this series is a collection of review articles published in 2023 that I found helpful. 

Property Prediction

Machine Learning Methods for Small Data Challenges in Molecular Science
https://pubs.acs.org/doi/full/10.1021/acs.chemrev.3c00189

Practical guidelines for the use of gradient boosting for molecular property prediction
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00743-7

Application of message passing neural networks for molecular property prediction
https://www.sciencedirect.com/science/article/pii/S0959440X23000908?via%3Dihub


Molecular Similarity

Molecular Similarity: Theory, Applications, and Perspectives
https://chemrxiv.org/engage/chemrxiv/article-details/655f59b15bc9fcb5c9354a43


Molecular Representation

From intuition to AI: evolution of small molecule representations in drug discovery
https://academic.oup.com/bib/article/25/1/bbad422/7455245


Docking and Scoring

The Impact of Supervised Learning Methods in Ultralarge High-Throughput Docking
https://pubs.acs.org/doi/10.1021/acs.jcim.2c01471

Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening
https://chemrxiv.org/engage/chemrxiv/article-details/654a339b48dad2312043870c

A practical guide to machine-learning scoring for structure-based virtual screening
https://www.nature.com/articles/s41596-023-00885-w

Keeping pace with the explosive growth of chemical libraries with structure-based virtual screening
https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.1678


Explainable AI

A Perspective on Explanations of Molecular Prediction Models
https://pubs.acs.org/doi/10.1021/acs.jctc.2c01235

Explainable AI for Bioinformatics: Methods, Tools and Applications
https://academic.oup.com/bib/article-abstract/24/5/bbad236/7227172?redirectedFrom=fulltext

From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery
https://pubs.acs.org/doi/10.1021/acs.jcim.3c01642


Generative Models

Integrating structure-based approaches in generative molecular design
https://www.sciencedirect.com/science/article/pii/S0959440X23000337

Deep generative models for 3D molecular structure
https://www.sciencedirect.com/science/article/pii/S0959440X23000404

Generative Models as an Emerging Paradigm in the Chemical Sciences
https://pubs.acs.org/doi/full/10.1021/jacs.2c13467


Open Source 

Open-Source Machine Learning in Computational Chemistry
https://pubs.acs.org/doi/10.1021/acs.jcim.3c00643


Multiple Instance Learning

Chemical complexity challenge: Is multi-instance machine learning a solution
https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.1698


Multi-objective Optimization

Computer-aided multi-objective optimization in small molecule discovery
https://www.cell.com/patterns/fulltext/S2666-3899(23)00001-6


Computational Approaches to Targeted Protein Degradation

Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods
https://pubs.acs.org/doi/10.1021/acs.jcim.3c00603


Data Related Reviews

Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data
https://pubs.acs.org/doi/10.1021/acs.jcim.3c00607







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