ReviewBiochimica et biophysica acta2015
You are lost without a map: Navigating the sea of protein structures.
Review in Biochimica et biophysica acta, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed.
- AI-Predicted Model-Guided Rebuilding of the Experimental Structure of Mouse δ-Aminolevulinic Acid Dehydratase.International journal of molecular sciences · 2026Article
- Article
- Temperature-Dependent Conformational Dynamics of Substrate Entrance Loops in β-Glucosidase: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2026Article
- A dual catalytic architecture promotes C-2 stereoinversion of CDP-glucose by the CDP-tyvelose 2-epimerase from Thermodesulfatator atlanticus.The Journal of biological chemistry · 2026Article
- Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach.Journal of cheminformatics · 2026Article
- Labeled dataset of X-ray protein ligand images in 3D point cloud and validated deep learning models.Scientific data · 2025Article
- Reuniting crystallography with real space: Ab initio structure elucidation with 4D-STEM.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Ascertaining a Structural Basis in Drug Discovery and Development.Journal of medicinal chemistry · 2025Article
- Article
- Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni.Scientific reports · 2024Article
- MatchMaps: Non-isomorphous difference maps for X-ray crystallography.bioRxiv : the preprint server for biology · 2024Article
- The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering.International journal of molecular sciences · 2023Review
- Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls.Journal of chemical information and modeling · 2022Article
- Snapshots of urea-induced early structural changes and unfolding of an ankyrin repeat protein at atomic resolution.Protein science : a publication of the Protein Society · 2022Article
- 'International journal of molecular sciences · 2021Article
- Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis.Journal of cheminformatics · 2019Article
- Article
- Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.Journal of molecular recognition : JMR · 2017Review
- Tools for ligand validation in Coot.Acta crystallographica. Section D, Structural biology · 2017Article
- Mg2+ ions: do they bind to nucleobase nitrogens?Nucleic acids research · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
X-ray crystal structures propel biochemistry research like no other experimental method, since they answer many questions directly and inspire new hypotheses. Unfortunately, many users of crystallographic models mistake them for actual experimental data. Crystallographic models are interpretations, several steps removed from the experimental measurements, making it difficult for nonspecialists to assess the quality of the underlying data. Crystallographers mainly rely on "global" measures of data and model quality to build models. Robust validation procedures based on global measures now largely ensure that structures in the Protein Data Bank (PDB) are largely correct. However, global measures do not allow users of crystallographic models to judge the reliability of "local" features in a region of interest. Refinement of a model to fit into an electron density map requires interpretation of the data to produce a single "best" overall model. This process requires inclusion of most probable conformations in areas of poor density. Users who misunderstand this can be misled, especially in regions of the structure that are mobile, including active sites, surface residues, and especially ligands. This article aims to equip users of macromolecular models with tools to critically assess local model quality. Structure users should always check the agreement of the electron density map and the derived model in all areas of interest, even if the global statistics are good. We provide illustrated examples of interpreted electron density as a guide for those unaccustomed to viewing electron density.
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.