ArticleJournal of chemical information and modeling2023
Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Discovery of non-nucleoside inhibitors of the enterovirus D68 3D polymerase through crystallographic fragment and high-throughput biochemical screening.bioRxiv : the preprint server for biology · 2026Article
- Developments and challenges in hit progression within fragment-based drug discovery.Nature communications · 2026Review
- Molecule generation for target protein binding with hierarchical consistency diffusion model.Chemical science · 2025Article
- Crystallographic Fragment Screening of the Dengue Virus Polymerase Reveals Multiple Binding Sites for the Development of Non-nucleoside Antiflavivirals.Journal of medicinal chemistry · 2025Article
- A New Fragment-Based Pharmacophore Virtual Screening Workflow Identifies Potent Inhibitors of SARS-CoV-2 NSP13 Helicase.Journal of computational chemistry · 2025Article
- Binding-Site Purification of Actives (B-SPA) Enables Efficient Large-Scale Progression of Fragment Hits by Combining Multi-Step Array Synthesis With HT Crystallography.Angewandte Chemie (International ed. in English) · 2025Article
- Structural Chemistry of Helicase Inhibition.Journal of medicinal chemistry · 2025Review
- Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open.RSC medicinal chemistry · 2025Article
- Fragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding-based methodology.Journal of cheminformatics · 2025Article
- Molecular similarity: Theory, applications, and perspectives.Artificial intelligence chemistry · 2024Article
- Geometry-complete diffusion for 3D molecule generation and optimization.Communications chemistry · 2024Article
- Article
- PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences.Chemical science · 2024Article
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Authors and funding
9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Fragment merging is a promising approach to progressing fragments directly to on-scale potency: each designed compound incorporates the structural motifs of overlapping fragments in a way that ensures compounds recapitulate multiple high-quality interactions. Searching commercial catalogues provides one useful way to quickly and cheaply identify such merges and circumvents the challenge of synthetic accessibility, provided they can be readily identified. Here, we demonstrate that the Fragment Network, a graph database that provides a novel way to explore the chemical space surrounding fragment hits, is well-suited to this challenge. We use an iteration of the database containing >120 million catalogue compounds to find fragment merges for four crystallographic screening campaigns and contrast the results with a traditional fingerprint-based similarity search. The two approaches identify complementary sets of merges that recapitulate the observed fragment-protein interactions but lie in different regions of chemical space. We further show our methodology is an effective route to achieving on-scale potency by retrospective analyses for two different targets; in analyses of public COVID Moonshot and
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