ArticleJournal of proteome research2013
Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples.
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 13 papers.
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Who cites it
13 citing papers in PubMed, 26 citations in OpenAlex.
- Cross-Linking Mass Spectrometry on P-Glycoprotein.International journal of molecular sciences · 2023Article
- Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology.Nature structural & molecular biology · 2018Review
- Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins.Nature protocols · 2018Article
- CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.Journal of proteome research · 2017Article
- ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.Journal of proteome research · 2016Article
- The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3-H4 tetramers and Asf1-H3-H4 complexes.Nucleic acids research · 2016Article
- ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database.BMC bioinformatics · 2016Article
- A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides.Molecular & cellular proteomics : MCP · 2016Article
- Protein Structural Analysis via Mass Spectrometry-Based Proteomics.Advances in experimental medicine and biology · 2016Review
- Organization of Subunits in the Membrane Domain of the Bovine F-ATPase Revealed by Covalent Cross-linking.The Journal of biological chemistry · 2015Article
- Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.Journal of structural biology · 2015Article
- Novel approaches to identify protein adducts produced by lipid peroxidation.Free radical research · 2015Review
- Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking.Mass spectrometry reviewsReview
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Chemical cross-linking of proteins combined with mass spectrometry provides an attractive and novel method for the analysis of native protein structures and protein complexes. Analysis of the data however is complex. Only a small number of cross-linked peptides are produced during sample preparation and must be identified against a background of more abundant native peptides. To facilitate the search and identification of cross-linked peptides, we have developed a novel software suite, named Hekate. Hekate is a suite of tools that address the challenges involved in analyzing protein cross-linking experiments when combined with mass spectrometry. The software is an integrated pipeline for the automation of the data analysis workflow and provides a novel scoring system based on principles of linear peptide analysis. In addition, it provides a tool for the visualization of identified cross-links using three-dimensional models, which is particularly useful when combining chemical cross-linking with other structural techniques. Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data. Further validation was carried out on known structural elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight into the previously uncharacterized C-terminal domain of the protein.
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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.