ArticleStructure (London, England : 1993)2022
Simplified quality assessment for small-molecule ligands in the Protein Data Bank.
Article in Structure (London, England : 1993), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Avoiding pitfalls when modelling ligands in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2026Article
- Learning a chemistry-aware latent space for molecular encoding and generation with a large-scale transformer variational autoencoder.Journal of cheminformatics · 2026Article
- Spacio-Linear Screening for Ligand-Docking Cavities in Protein Structures: SLAM Algorithm.Life (Basel, Switzerland) · 2026Article
- A fully automated benchmarking suite to compare macromolecular complexes.Nature methods · 2026Review
- Denoising and iterative phase recovery reveal low-occupancy populations in protein crystals.Communications biology · 2025Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank.Genomics, proteomics & bioinformatics · 2025Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Computational exploration ofBiochemistry and biophysics reports · 2024Article
- PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences.Chemical science · 2024Article
- The ACPYPE web server for small-molecule MD topology generation.Bioinformatics (Oxford, England) · 2023Article
- Tautomer-Specific Deacylation and Ω-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 β-Lactamase.Journal of the American Chemical Society · 2023Article
- Article
- RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
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12 authors.
Funding
Abstract
More than 70% of the experimentally determined macromolecular structures in the Protein Data Bank (PDB) contain small-molecule ligands. Quality indicators of ∼643,000 ligands present in ∼106,000 PDB X-ray crystal structures have been analyzed. Ligand quality varies greatly with regard to goodness of fit between ligand structure and experimental data, deviations in bond lengths and angles from known chemical structures, and inappropriate interatomic clashes between the ligand and its surroundings. Based on principal component analysis, correlated quality indicators of ligand structure have been aggregated into two largely orthogonal composite indicators measuring goodness of fit to experimental data and deviation from ideal chemical structure. Ranking of the composite quality indicators across the PDB archive enabled construction of uniformly distributed composite ranking score. This score is implemented at RCSB.org to compare chemically identical ligands in distinct PDB structures with easy-to-interpret two-dimensional ligand quality plots, allowing PDB users to quickly assess ligand structure quality and select the best exemplars.
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