ArticleJournal of proteome research2015
Kojak: efficient analysis of chemically cross-linked protein complexes.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
What it found
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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
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Who cites it
97 citing papers in PubMed, 200 citations in OpenAlex.
- XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry.Nature communications · 2026Article
- AIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching.Analytical chemistry · 2025Article
- Disorder with consequence: Phosphorylation sites in HSPB5 yield distinct structural outcomes.bioRxiv : the preprint server for biology · 2025Article
- Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.Nature communications · 2025Article
- Article
- Activation mechanism of small heat shock protein HSPB5 revealed by disease-associated mutants.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.Communications chemistry · 2024Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid.Journal of proteome research · 2024Article
- An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics.Bioinformatics (Oxford, England) · 2024Article
- CLAUDIO: automated structural analysis of cross-linking data.Bioinformatics (Oxford, England) · 2024Article
- Article
- Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry.Molecular & cellular proteomics : MCP · 2023Article
- ECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis.BMC bioinformatics · 2023Article
- MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity.Journal of proteome research · 2023Article
- Determination of Protein Monoclonal-Antibody Epitopes by a Combination of Structural Proteomics Methods.Journal of proteome research · 2023Article
- BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation.The EMBO journal · 2023Article
- High-Sensitivity Proteome-Scale Searches for Crosslinked Peptides Using CRIMP 2.0.Analytical chemistry · 2023Article
- High-resolution structural information of membrane-bound α-synuclein provides insight into the MoA of the anti-Parkinson drug UCB0599.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Disordered region encodes α-crystallin chaperone activity toward lens client γD-crystallin.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Protein chemical cross-linking and mass spectrometry enable the analysis of protein-protein interactions and protein topologies; however, complicated cross-linked peptide spectra require specialized algorithms to identify interacting sites. The Kojak cross-linking software application is a new, efficient approach to identify cross-linked peptides, enabling large-scale analysis of protein-protein interactions by chemical cross-linking techniques. The algorithm integrates spectral processing and scoring schemes adopted from traditional database search algorithms and can identify cross-linked peptides using many different chemical cross-linkers with or without heavy isotope labels. Kojak was used to analyze both novel and existing data sets and was compared to existing cross-linking algorithms. The algorithm provided increased cross-link identifications over existing algorithms and, equally importantly, the results in a fraction of computational time. The Kojak algorithm is open-source, cross-platform, and freely available. This software provides both existing and new cross-linking researchers alike an effective way to derive additional cross-link identifications from new or existing data sets. For new users, it provides a simple analytical resource resulting in more cross-link identifications than other methods.
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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.