ArticleJournal of chemical information and modeling2020
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 11 citations in OpenAlex.
- Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites.Journal of chemical information and modeling · 2024Article
- Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2.Journal of chemical information and modeling · 2024Article
- Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors.Journal of chemical information and modeling · 2022Article
- API Development Increases Access to Shared Computing Resources at Boston University.Journal of software engineering and applications · 2022Article
- Fragment-to-Lead Medicinal Chemistry Publications in 2020.Journal of medicinal chemistry · 2022Review
- Common recognition topology of mex transporters ofFrontiers in pharmacology · 2022Article
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Authors and funding
8 authors at 5 institutions in 3 countries.
Funding
Abstract
Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. Each protein structure in the set binds a fragment, which is extended into larger ligands in other structures without substantial change in its binding mode. Structures of the same proteins without any bound ligand are also collected to form an unbound benchmark. We also discuss a set developed by Astex Pharmaceuticals for the validation of hot and warm spots for fragment binding. The set is based on the assumption that a fragment that occurs in diverse ligands in the same subpocket identifies a binding hot spot. Since this set includes only ligand-bound proteins, we added a set with unbound structures. All four sets were tested using FTMap, a computational analogue of fragment screening experiments to form a baseline for testing other prediction methods, and differences among the sets are discussed.
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Registered trials
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