ArticleStructure (London, England : 1993)2021
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.
Article in Structure (London, England : 1993), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- Avoiding pitfalls when modelling ligands in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2026Article
- Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution.Acta crystallographica. Section D, Structural biology · 2026Article
- Article
- Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps.Acta crystallographica. Section D, Structural biology · 2025Article
- PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank.Protein science : a publication of the Protein Society · 2025Article
- Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study.Protein science : a publication of the Protein Society · 2025Article
- Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.Database : the journal of biological databases and curation · 2024Article
- Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them.Acta crystallographica. Section D, Structural biology · 2024Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.Structure (London, England : 1993) · 2024Article
- EMDB-the Electron Microscopy Data Bank.Nucleic acids research · 2024Review
- Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership.Acta crystallographica. Section D, Structural biology · 2023Article
- Review
- RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.Nucleic acids research · 2023Article
- RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level.Structure (London, England : 1993) · 2022Article
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- Exploring protein symmetry at the RCSB Protein Data Bank.Emerging topics in life sciences · 2022Article
- Simplified quality assessment for small-molecule ligands in the Protein Data Bank.Structure (London, England : 1993) · 2022Article
- 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
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package. Augmented wwPDB validation report features include: two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation outcomes; 2D topological diagrams of oligosaccharides present in branched entities generated using 2D Symbol Nomenclature for Glycan representation; and views of 3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental data (X-ray crystallographic structures only). These improvements will impact confidence in ligand conformation and ligand-macromolecular interactions that will aid in understanding biochemical function and contribute to small-molecule drug discovery.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.