ArticleNucleic acids research2021
CoV3D: a database of high resolution coronavirus protein structures.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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
45 citing papers in PubMed.
- Paraplume: A fast and accurate antibody paratope prediction method provides insights into repertoire-scale binding dynamics.PLoS computational biology · 2026Article
- Proteomic Analysis of COVID-19 Infection.Advances in experimental medicine and biology · 2026Article
- Corona VRus Coaster: the virtual reality roller coaster of the proteins of SARS-CoV-2.Journal of molecular modeling · 2025Article
- Exploring the Intrinsic Structural Plasticity and Conformational Dynamics of Human Beta Coronavirus Spike Glycoproteins.Journal of chemical information and modeling · 2025Article
- A fast approach for structural and evolutionary analysis based on energetic profile protein comparison.Nature communications · 2025Article
- MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions.Protein science : a publication of the Protein Society · 2024Article
- Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.PLoS computational biology · 2024Article
- CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses.Briefings in bioinformatics · 2024Article
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- Surfaces: a software to quantify and visualize interactions within and between proteins and ligands.Bioinformatics (Oxford, England) · 2023Article
- The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion.JCI insight · 2023Article
- Early warning of emerging infectious diseases based on multimodal data.Biosafety and health · 2023Review
- Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design.Pathogens and global health · 2023Review
- Structure-free antibody paratope similarity prediction foriScience · 2023Article
- SARS-CoV-2 Omicron Subvariants Balance Host Cell Membrane, Receptor, and Antibody Docking via an Overlapping Target Site.Viruses · 2023Article
- Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD.iScience · 2023Article
- Applying the digital data and the bioinformatics tools in SARS-CoV-2 research.Computational and structural biotechnology journal · 2023Review
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Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
SARS-CoV-2, the etiologic agent of COVID-19, exemplifies the general threat to global health posed by coronaviruses. The urgent need for effective vaccines and therapies is leading to a rapid rise in the number of high resolution structures of SARS-CoV-2 proteins that collectively reveal a map of virus vulnerabilities. To assist structure-based design of vaccines and therapeutics against SARS-CoV-2 and other coronaviruses, we have developed CoV3D, a database and resource for coronavirus protein structures, which is updated on a weekly basis. CoV3D provides users with comprehensive sets of structures of coronavirus proteins and their complexes with antibodies, receptors, and small molecules. Integrated molecular viewers allow users to visualize structures of the spike glycoprotein, which is the major target of neutralizing antibodies and vaccine design efforts, as well as sets of spike-antibody complexes, spike sequence variability, and known polymorphisms. In order to aid structure-based design and analysis of the spike glycoprotein, CoV3D permits visualization and download of spike structures with modeled N-glycosylation at known glycan sites, and contains structure-based classification of spike conformations, generated by unsupervised clustering. CoV3D can serve the research community as a centralized reference and resource for spike and other coronavirus protein structures, and is available at: https://cov3d.ibbr.umd.edu.
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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.