ArticleJournal of proteome research2023
Sequence Coverage Visualizer: A Web Application for Protein Sequence Coverage 3D Visualization.
Article in Journal of proteome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Phosphoproteomic Landscape of HDLBP: Insights into Function and Disease Associations.International journal of molecular sciences · 2026Article
- Phosphoproteome landscape of ARID1A and its implications in DNA damage response and breast cancer pathogenesis.Discover oncology · 2026Article
- Revealing RELL1 signaling relying on the phosphoregulatory network analysis.Frontiers in bioinformatics · 2026Article
- Integrative analysis of YTHDC1 phosphoproteome unveils its phosphomodulatory network linked to splicing and tumorigenesis.Frontiers in bioinformatics · 2026Article
- Integrative phosphoproteomics reveals kinase-mediated regulation of OCIAD1 and its roles in mitochondrial quality control.Frontiers in bioinformatics · 2026Article
- Phosphoregulation of interleukin-1 receptor-associated kinase 1 in inflammatory signaling.Frontiers in immunology · 2026Review
- Phosphorylation Sites of the Gastric Inhibitory Polypeptide Receptor (GIPR) Revealed by Trapped-Ion-Mobility Spectrometry Coupled to Time-of-Flight Mass Spectrometry (TIMS-TOF MS).Journal of the American Chemical Society · 2023Article
- Exosomal PPARγ derived from macrophages suppresses LPS-induced peritonitis by negative regulation of CD14/TLR4 axis.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2023Article
- Identification and quantification of protein nitration sites in human coronary artery smooth muscle cells in the absence and presence of peroxynitrous acid/peroxynitrite.Redox biology · 2023Article
- MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database.Nucleic acids research · 2023Article
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Authors and funding
3 authors.
Funding
Abstract
Protein structure defines protein function and plays an extremely important role in protein characterization. Recently, two groups of researchers from DeepMind and the Baker lab have independently published protein structure prediction tools that can help us obtain predicted protein structures for the whole human proteome. This enabled us to visualize the entire human proteome using predicted 3D structures for the first time. To help other researchers best utilize these protein structure predictions in proteomics experiments, we present the Sequence Coverage Visualizer (SCV), http://scv.lab.gy, a web application for protein sequence coverage 3D visualization. Here we showed a few possible usages of the SCV, including the labeling of post-translational modifications and isotope labeling experiments. These results highlight the usefulness of such 3D visualization for proteomics experiments and how SCV can turn a regular proteomics experiment (identified peptide list) into structural insights. Furthermore, when used together with limited proteolysis, we demonstrated that SCV can help to compare different protein structures from different sources, including predicted ones and existing PDB entries. We hope our tool can provide help in the process of improving protein structure prediction accuracy. Overall, SCV is a convenient and powerful tool for visualizing proteomics results in 3D.
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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.