ArticleBioinformatics (Oxford, England)2023
MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- An interpretable framework applying protein words to predict protein-small molecule complementary pairing rules.Chemical science · 2026Article
- Revisiting molecular descriptors with TDiMS for interpretable intramolecular interactions based on substructure pairs.Nature computational science · 2026Article
- CRUSH-Cleavage Rules Using SMIRKS Heuristics: an enhanced molecular fragmentation algorithm.Journal of cheminformatics · 2026Article
- Molecular Design with Artificial Intelligence: Progress and Perspectives for Small Molecules.Chemical reviews · 2026Review
- APPi: A Multiscale Qualitative-Quantitative Insecticide-Likeness Evaluation Platform and Application.Plant biotechnology journal · 2025Article
- Exploring the macrocyclic chemical space for heuristic drug design with deep learning models.Communications chemistry · 2025Article
- Article
- Multiscale biased chemical space remodeling for developing APLNR agonists with anti-HFpEF efficacy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Group graph: a molecular graph representation with enhanced performance, efficiency and interpretability.Journal of cheminformatics · 2024Article
- DigFrag as a digital fragmentation method used for artificial intelligence-based drug design.Communications chemistry · 2024Article
- Molecular fragmentation as a crucial step in the AI-based drug development pathway.Communications chemistry · 2024Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
summaryConstruction of high-quality fragment libraries by segmenting organic compounds is an important part of the drug discovery paradigm. This article presents a new method, MacFrag, for efficient molecule fragmentation. MacFrag utilized a modified version of BRICS rules to break chemical bonds and introduced an efficient subgraphs extraction algorithm for rapid enumeration of the fragment space. The evaluation results with ChEMBL dataset exhibited that MacFrag was overall faster than BRICS implemented in RDKit and modified molBLOCKS. Meanwhile, the fragments acquired through MacFrag were more compliant with the 'Rule of Three'. AVAILABILITY AND IMPLEMENTATION: https://github.com/yydiao1025/MacFrag. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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