ArticleJournal of cheminformatics2021
"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool.
Article in Journal of cheminformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- An effective fragment-based dual conditional diffusion framework for molecular generation.Briefings in bioinformatics · 2026Article
- Molecular deep learning at the edge of chemical space.Nature machine intelligence · 2026Article
- Discovery of Potential Antileishmanial Compounds Through Phenotypic Screening of an Alkaloid Library.Molecules (Basel, Switzerland) · 2025Article
- Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation.Nature communications · 2025Article
- Role of Artificial Intelligence in Drug Discovery to Revolutionize the Pharmaceutical Industry: Resources, Methods and Applications.Recent patents on biotechnology · 2025Review
- "DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases.Journal of cheminformatics · 2024Article
- PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.Journal of cheminformatics · 2023Article
- NMR-Verified Dearomatization of 5,7-Substituted Pyrazolo[1,5-a]pyrimidines.Molecules (Basel, Switzerland) · 2023Article
- ProfhEX: AI-based platform for small molecules liability profiling.Journal of cheminformatics · 2023Article
- Artificial intelligence for drug discovery: Resources, methods, and applications.Molecular therapy. Nucleic acids · 2023Review
- Cheminformatic Analysis and Machine Learning Modeling to Investigate Androgen Receptor Antagonists to Combat Prostate Cancer.ACS omega · 2023Article
- Exploring the Chemical Space of CYP17A1 Inhibitors Using Cheminformatics and Machine Learning.Molecules (Basel, Switzerland) · 2023Article
- Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK).Journal of cheminformatics · 2022Article
- AnArtificial intelligence in the life sciences · 2021Article
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Authors and funding
7 authors.
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Abstract
The scaffold representation is widely employed to classify bioactive compounds on the basis of common core structures or correlate compound classes with specific biological activities. In this paper, we present a novel approach called "Molecular Anatomy" as a flexible and unbiased molecular scaffold-based metrics to cluster large set of compounds. We introduce a set of nine molecular representations at different abstraction levels, combined with fragmentation rules, to define a multi-dimensional network of hierarchically interconnected molecular frameworks. We demonstrate that the introduction of a flexible scaffold definition and multiple pruning rules is an effective method to identify relevant chemical moieties. This approach allows to cluster together active molecules belonging to different molecular classes, capturing most of the structure activity information, in particular when libraries containing a huge number of singletons are analyzed. We also propose a procedure to derive a network visualization that allows a full graphical representation of compounds dataset, permitting an efficient navigation in the scaffold's space and significantly contributing to perform high quality SAR analysis. The protocol is freely available as a web interface at https://ma.exscalate.eu .
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