ArticleStructural dynamics (Melville, N.Y.)2017
Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.
Article in Structural dynamics (Melville, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Article
- A resource-efficient structure-based workflow for fragment progression enables parallel hit discovery and validation of functionally diverse modulators of NCS-1 protein-protein interactions.Chemical science · 2026Article
- An integrated experimental and computational pipeline for crystallographic fragment screening of membrane protein in the lipid cubic phase.Communications chemistry · 2026Article
- Crystallographic Fragment Screening of the Dengue Virus Polymerase Reveals Multiple Binding Sites for the Development of Non-nucleoside Antiflavivirals.Journal of medicinal chemistry · 2025Article
- Crystallographic fragment screening reveals ligand hotspots in TRIM21 PRY-SPRY domain.Communications chemistry · 2025Article
- Critical assessment of LC3/GABARAP ligands used for degrader development and ligandability of LC3/GABARAP binding pockets.Nature communications · 2024Article
- High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms.Acta crystallographica. Section D, Structural biology · 2024Article
- Controlling the incorporation of fluorinated amino acids in human cells and its structural impact.Protein science : a publication of the Protein Society · 2024Article
- Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.Acta crystallographica. Section D, Structural biology · 2024Article
- A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.Nature communications · 2023Article
- Crystal polymorphism in fragment-based lead discovery of ligands of the catalytic domain of UGGT, the glycoprotein folding quality control checkpoint.Frontiers in molecular biosciences · 2022Article
- Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.Frontiers in molecular biosciences · 2022Article
- Fragment-Based Ligand Discovery Applied to the Mycolic Acid Methyltransferase Hma (MmaA4) fromPharmaceuticals (Basel, Switzerland) · 2021Article
- Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.Angewandte Chemie (International ed. in English) · 2021Article
- Guest-protein incorporation into solvent channels of a protein host crystal (hostal).Acta crystallographica. Section D, Structural biology · 2021Article
- qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps.Protein science : a publication of the Protein Society · 2021Article
- Discovery of allosteric binding sites by crystallographic fragment screening.Current opinion in structural biology · 2020Review
- Protein X-ray Crystallography and Drug Discovery.Molecules (Basel, Switzerland) · 2020Review
- Advances in methods for atomic resolution macromolecular structure determination.F1000Research · 2020Review
- Predicting protein-ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A.Chemical science · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Crystallographic fragment screening uses low molecular weight compounds to probe the protein surface and although individual protein-fragment interactions are high quality, fragments commonly bind at low occupancy, historically making identification difficult. However, our new Pan-Dataset Density Analysis method readily identifies binders missed by conventional analysis: for fragment screening data of lysine-specific demethylase 4D (KDM4D), the hit rate increased from 0.9% to 10.6%. Previously unidentified fragments reveal multiple binding sites and demonstrate: the versatility of crystallographic fragment screening; that surprisingly large conformational changes are possible in crystals; and that low crystallographic occupancy does not by itself reflect a protein-ligand complex's significance.
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