ArticleJournal of proteome research2013
XLink-DB: database and software tools for storing and visualizing protein interaction topology data.
Article in Journal of proteome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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.
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Who cites it
38 citing papers in PubMed.
- Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS.Nature communications · 2026Article
- Integrative structure determination of a human mitochondrial contact site and cristae organizing system (MICOS) sub-assembly.bioRxiv : the preprint server for biology · 2026Article
- CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2.Nature methods · 2024Article
- Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS.Journal of proteome research · 2023Article
- Predicting structures of large protein assemblies using combinatorial assembly algorithm and AlphaFold2.bioRxiv : the preprint server for biology · 2023Article
- Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking Mass Spectrometry (AP-XL-MS) based Proteomics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Improved Interpretation of Protein Conformational Differences and Ligand Occupancy in Large-Scale Cross-Link Data.Journal of proteome research · 2022Article
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- Applications and advancements of FT-ICR-MS for interactome studies.Mass spectrometry reviews · 2022Review
- Crosslinking mass spectrometry: A link between structural biology and systems biology.Protein science : a publication of the Protein Society · 2021Review
- Leveraging the Entirety of the Protein Data Bank to Enable Improved Structure Prediction Based on Cross-Link Data.Journal of proteome research · 2021Article
- Quantitative Cross-Linking of Proteins and Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Proteomics in Non-model Organisms: A New Analytical Frontier.Journal of proteome research · 2020Article
- In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes.Journal of the American Society for Mass Spectrometry · 2020Article
- Cellular Interactome Dynamics during Paclitaxel Treatment.Cell reports · 2019Article
- Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.Journal of proteome research · 2019Article
- Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks.Bioinformatics (Oxford, England) · 2019Article
- Tools for 3D Interactome Visualization.Journal of proteome research · 2019Article
- Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates.Journal of proteome research · 2019Article
- Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology.Nature structural & molecular biology · 2018Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
As large-scale cross-linking data becomes available, new software tools for data processing and visualization are required to replace manual data analysis. XLink-DB serves as a data storage site and visualization tool for cross-linking results. XLink-DB accepts data generated with any cross-linker and stores them in a relational database. Cross-linked sites are automatically mapped onto PDB structures if available, and results are compared to existing protein interaction databases. A protein interaction network is also automatically generated for the entire data set. The XLink-DB server, including examples, and a help page are available for noncommercial use at http://brucelab.gs.washington.edu/crosslinkdbv1/ . The source code can be viewed and downloaded at https://sourceforge.net/projects/crosslinkdb/?source=directory .
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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.