ArticleProtein science : a publication of the Protein Society2018
Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed.
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- A Critical Look at the Crystal Structures of cAMP-Dependent Protein Kinases.Kinases and phosphatases · 2025Article
- Structural and biochemical characterisation of CoChemical science · 2023Article
- Tip60 acetylation of histone H3K4 temporally controls chromosome passenger complex localization.Molecular biology of the cell · 2022Article
- Group depositions to the Protein Data Bank need adequate presentation and different archiving protocol.Protein science : a publication of the Protein Society · 2022Article
- Detecting anomalies in X-ray diffraction images using convolutional neural networks.Expert systems with applications · 2021Article
- Recognizing and validating ligands with CheckMyBlob.Nucleic acids research · 2021Article
- A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.The FEBS journal · 2021Article
- Gcn5-RelatedFrontiers in molecular biosciences · 2021Article
- Article
- Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank.The FEBS journal · 2020Article
- Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy.bioRxiv : the preprint server for biology · 2020Article
- Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma.Journal of medicinal chemistry · 2020Article
- On the evolution of the quality of macromolecular models in the PDB.The FEBS journal · 2020Article
- Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.The FEBS journal · 2020Article
- Regioselectivity of hyoscyamine 6β-hydroxylase-catalysed hydroxylation as revealed by high-resolution structural information and QM/MM calculations.Dalton transactions (Cambridge, England : 2003) · 2020Article
- Molstack: A platform for interactive presentations of electron density and cryo-EM maps and their interpretations.Protein science : a publication of the Protein Society · 2020Article
- Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.International journal of biological macromolecules · 2019Article
- Testosterone meets albumin - the molecular mechanism of sex hormone transport by serum albumins.Chemical science · 2019Article
- Automatic recognition of ligands in electron density by machine learning.Bioinformatics (Oxford, England) · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼90% are an interpretation of electron density maps. This structural information guides scientific progress and exploration in many biomedical disciplines. The Protein Data Bank's web portals have made these structures available for mass scientific consumption and greatly broaden the scope of information presented in scientific publications. The portals provide numerous quality metrics; however, the portion of the structure that is most vital for interpretation of the function may have the most difficult to interpret electron density and this ambiguity is not reflected by any single metric. The possible consequences of basing research on suboptimal models make it imperative to inspect the agreement of a model with its experimental evidence. Molstack, a web-based interactive publishing platform for structural data, allows users to present density maps and structural models by displaying a collection of maps and models, including different interpretation of one's own data, re-refinements, and corrections of existing structures. Molstack organizes the sharing and dissemination of these structural models along with their experimental evidence as an interactive session. Molstack was designed with three groups of users in mind; researchers can present the evidence of their interpretation, reviewers and readers can independently judge the experimental evidence of the authors' conclusions, and other researchers can present or even publish their new hypotheses in the context of prior results. The server is available at http://molstack.bioreproducibility.org.
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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.