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Literature DB >> 23413830

XLink-DB: database and software tools for storing and visualizing protein interaction topology data.

Chunxiang Zheng¹, Chad R Weisbrod, Juan D Chavez, Jimmy K Eng, Vagisha Sharma, Xia Wu, James E Bruce.

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 .

Entities: Chemical Species

Mesh：

Substances：

Year: 2013 PMID： 23413830 PMCID： PMC3744611 DOI： 10.1021/pr301162j

Source DB: PubMed Journal: J Proteome Res ISSN： 1535-3893 Impact factor: 4.466

32 in total

1. Algorithms for identifying protein cross-links via tandem mass spectrometry.

Authors: T Chen; J D Jaffe; G M Church
Journal: J Comput Biol Date: 2001 Impact factor: 1.479

Review 2. Chemical cross-linking and mass spectrometry for protein structural modeling.

Authors: Jaap Willem Back; Luitzen de Jong; Anton O Muijsers; Chris G de Koster
Journal: J Mol Biol Date: 2003-08-08 Impact factor: 5.469

3. Mapping spatial proximities of sulfhydryl groups in proteins using a fluorogenic cross-linker and mass spectrometry.

Authors: Andrea Sinz; Kuan Wang
Journal: Anal Biochem Date: 2004-08-01 Impact factor: 3.365

4. False discovery rate estimation for cross-linked peptides identified by mass spectrometry.

Authors: Thomas Walzthoeni; Manfred Claassen; Alexander Leitner; Franz Herzog; Stefan Bohn; Friedrich Förster; Martin Beck; Ruedi Aebersold
Journal: Nat Methods Date: 2012-07-08 Impact factor: 28.547

Review 5. Analysis of protein complexes using mass spectrometry.

Authors: Anne-Claude Gingras; Matthias Gstaiger; Brian Raught; Ruedi Aebersold
Journal: Nat Rev Mol Cell Biol Date: 2007-08 Impact factor: 94.444

6. Identification of cross-linked peptides from large sequence databases.

Authors: Oliver Rinner; Jan Seebacher; Thomas Walzthoeni; Lukas N Mueller; Martin Beck; Alexander Schmidt; Markus Mueller; Ruedi Aebersold
Journal: Nat Methods Date: 2008-03-09 Impact factor: 28.547

7. Mapping cross-linking sites in modified proteins with mass spectrometry: an application to cross-linked hemoglobins.

Authors: T Yang; D R Horejsh; K J Mahan; E J Zaluzec; T J Watson; D A Gage
Journal: Anal Biochem Date: 1996-11-01 Impact factor: 3.365

8. Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions.

Authors: Juan D Chavez; Michelle Cilia; Chad R Weisbrod; Ho-Jong Ju; Jimmy K Eng; Stewart M Gray; James E Bruce
Journal: J Proteome Res Date: 2012-03-30 Impact factor: 4.466

9. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.

Authors: M M Young; N Tang; J C Hempel; C M Oshiro; E W Taylor; I D Kuntz; B W Gibson; G Dollinger
Journal: Proc Natl Acad Sci U S A Date: 2000-05-23 Impact factor: 11.205

10. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.

Authors: Zhuo Angel Chen; Anass Jawhari; Lutz Fischer; Claudia Buchen; Salman Tahir; Tomislav Kamenski; Morten Rasmussen; Laurent Lariviere; Jimi-Carlo Bukowski-Wills; Michael Nilges; Patrick Cramer; Juri Rappsilber
Journal: EMBO J Date: 2010-01-21 Impact factor: 11.598

30 in total

1. Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.

Authors: Andrew Keller; Juan D Chavez; Kevin C Felt; James E Bruce
Journal: J Proteome Res Date: 2019-07-17 Impact factor: 4.466

Review 2. Chemical cross-linking in the structural analysis of protein assemblies.

Authors: Feixia Chu; Daniel T Thornton; Hieu T Nguyen
Journal: Methods Date: 2018-05-30 Impact factor: 3.608

3. Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers.

Authors: Xuefei Zhong; Arti T Navare; Juan D Chavez; Jimmy K Eng; Devin K Schweppe; James E Bruce
Journal: J Proteome Res Date: 2016-11-30 Impact factor: 4.466

XLink-DB: database and software tools for storing and visualizing protein interaction topology data.

1. Algorithms for identifying protein cross-links via tandem mass spectrometry.

Review 2. Chemical cross-linking and mass spectrometry for protein structural modeling.

3. Mapping spatial proximities of sulfhydryl groups in proteins using a fluorogenic cross-linker and mass spectrometry.

4. False discovery rate estimation for cross-linked peptides identified by mass spectrometry.

Review 5. Analysis of protein complexes using mass spectrometry.

6. Identification of cross-linked peptides from large sequence databases.

7. Mapping cross-linking sites in modified proteins with mass spectrometry: an application to cross-linked hemoglobins.

8. Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions.

9. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.

10. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.

1. Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.

Review 2. Chemical cross-linking in the structural analysis of protein assemblies.

3. Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers.

4. Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates.

5. Quantitative Cross-Linking of Proteins and Protein Complexes.

6. Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b₅₅₉ in Photosystem II.

7. Protein interactions, post-translational modifications and topologies in human cells.

8. CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

9. In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy.

10. In Vivo Conformational Dynamics of Hsp90 and Its Interactors.