ArticleActa crystallographica. Section D, Structural biology2018
Validation of ligands in macromolecular structures determined by X-ray crystallography.
Article in Acta crystallographica. Section D, Structural biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed, 80 citations in OpenAlex.
- Avoiding pitfalls when modelling ligands in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2026Article
- Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach.Journal of cheminformatics · 2026Article
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- Denoising and iterative phase recovery reveal low-occupancy populations in protein crystals.Communications biology · 2025Article
- Halogen bonds between ligands and proteins: Can we use them in validation?Protein science : a publication of the Protein Society · 2025Article
- Article
- Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome.bioRxiv : the preprint server for biology · 2025Article
- Article
- Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments.bioRxiv : the preprint server for biology · 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
- PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank.Protein science : a publication of the Protein Society · 2025Article
- Ligand identification in CryoEM and X-ray maps using deep learning.Bioinformatics (Oxford, England) · 2024Article
- Ligand Identification in CryoEM and X-ray Maps Using Deep Learning.bioRxiv : the preprint server for biology · 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
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
- Development of Novel Small-Molecule Activators of Pyruvate Kinase Muscle Isozyme 2, PKM2, to Reduce Photoreceptor Apoptosis.Pharmaceuticals (Basel, Switzerland) · 2023Article
- CMM-An enhanced platform for interactive validation of metal binding sites.Protein science : a publication of the Protein Society · 2023Article
- Structures of multisubunit membrane complexes with the CRYO ARM 200.Microscopy (Oxford, England) · 2022Article
- Structure and mechanism of the bacterial lipid ABC transporter, MlaFEDB.Current opinion in structural biology · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or represents water or buffer molecules is often far from trivial. The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. The ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.
Indexed as
Identifiers
What OpenQuestion holds
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.