If you use XLinkDB to review or manage data, please cite:

XLink-DB 4.0: Integrated, large-scale structural analysis of protein crosslinking data.
Devin K Schweppe , Chunxiang Zheng , Juan D Chavez , Arti T Navare , Xia Wu , Jimmy K Eng , and James E Bruce Bioinformatics. DOI:10.1093/bioinformatics/btw232


XLink-DB: database and software tools for storing and visualizing protein interaction topology data.
Chunxiang Zheng , Chad R Weisbrod , Juan D Chavez , Jimmy K Eng , Vagisha Sharma , Xia Wu , and James E Bruce J. Proteome Res. DOI:10.1021/pr301162j


Visit the Bruce Lab website for related pubications.



Citations for public data and tools used in XLinkDB 4.0 can be found here:


Network and Structural Tools:

Integrative Modeling Pipeline (IMP): Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies.
Daniel Russel, Keren Lasker, Ben Webb, Javier Velazquez-Muriel, Elina Tjioe, Dina Schneidman-Duhovny, Bret Peterson, and Andrej Sali
PLoS Biology, (2012) 10(1): e1001244. | doi:10.1371/journal.pbio.1001244


xiNET: xiNET: cross-link network maps with residue resolution.
Colin W Combe, Lutz Fischer, and Juri Rappsilber
Molecular and Cellular Proteomics, April 1, 2015 Molecular & Cellular Proteomics, 14, 1137-1147. | doi:10.1074/mcp.O114.042259


Cytoscape.js: Cytoscape.js: a graph theory library for visualisation and analysis.
Max Franz, Christian T. Lopes, Gerardo Huck, Yue Dong, Onur Sumer, and Gary D. Bader
Bioinformatics, (2010) 26 (18): 2347-2348. | doi:10.1093/bioinformatics/btq430


Cytoscape Web: Cytoscape Web: an interactive web-based network browser.
Christian T. Lopes, Max Franz, Farzana Kazi, Sylva L. Donaldson, Quaid Morris, and Gary D. Bader
Bioinformatics, (2016) 32 (2): 309-311. | 10.1093/bioinformatics/btv557



XL-MS Interaction Networks:

HeLa_PTX_titration_Cell_Reports_2019: Cellular interactome dynamics during paclitaxel treatment.
Juan D. Chavez, Andrew Keller, Bo Zhou, Rong Tian, and James E. Bruce
Cell Reports. Volume 29, Issue 8, P2371-2383.E5, Nov 19, 2019. PMID: 31747606


KellerJProteomeRes2019_HeLaInVivo_Bruce/KellerJProteomeRes2019_HeLaLysate_Bruce: Prediction of an Upper Limit for the Fraction of Inter-Protein Cross-Links in Large-scale In Vivo Cross-Linking Studies.
Andrew Keller, Juan D. Chavez, Kevin C. Felt, and James E. Bruce
J Proteome Res. 2019 Jul 3. doi: 10.1021/acs.jproteome.9b00189. PMID: 31267744


KellerJProteomeRes2019_HeLaInVivo_Bruce/KellerJProteomeRes2019_HeLaLysate_Bruce: Prediction of an Upper Limit for the Fraction of Inter-Protein Cross-Links in Large-scale In Vivo Cross-Linking Studies.
Andrew Keller, Juan D. Chavez, Kevin C. Felt, and James E. Bruce
J Proteome Res. 2019 Jul 3. doi: 10.1021/acs.jproteome.9b00189. PMID: 31267744


KellerBioinformatics2018_Bruce: Increased Sensitivity with Automated Validation of XL-MS Cleavable Peptide Crosslinks.
Andrew Keller, Juan D Chavez, and James E Bruce
Bioinformatics, bty720, Published online 20 August 2018. PMID: 30137231


SchweppemousemitoPNAS2017_BruceLab: Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry.
Devin K Schweppe, Juan Chavez, CF Lee, A Caudal, SE Kruse, R Stuppard, DJ Marcinek, GS Shadel, R Tian, and James E Bruce
Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1732-1737. PMID: 28130547


ChavezChemBiol2016_BruceLab: In vivo conformational dynamics of Hsp90 and its interactors.
Juan Chavez, Devin K Schweppe, Jimmy K Eng and James E Bruce
Cell Chemical Biology, Cell Chem Biol. 2016 Jun 23;23(6):716-726 PMID: 27341434


Wu_NatureComm2016_BruceLab: In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in antibiotic resistant bacteria.
Xia Wu, Juan Chavez, Devin Schweppe, Chunxiang Zheng, Chad Weisbrod, Jimmy Eng, Ananya Murali, Samuel Lee, Elizabeth Ramage, Larry Gallagher, Hematha Kulasekara, Mauna Edrozo, Cassandra Kamischke, Mitchell Brittnacher, Samuel Miller, Pradeep Singh, Colin Manoil, and James Bruce
Nature Communications Nov 11;7:13414 PMID: 27834373


ChavezChemBiol2016_BruceLab: In Vivo Conformational Dynamics of Hsp90 and Its Interactors.
Juan D. Chavez, Devin K. Schweppe, Jimmy K. Eng, James E. Bruce
Cell Chemical Biology,Volume 23, Issue 6, 23 June 2016, Pages 716–726 | doi:10.1016/j.chembiol.2016.05.012


Schweppe2015ChemBio_BruceLab: Host-Microbe Protein Interactions during Bacterial Infection.
Devin K. Schweppe, Christopher Harding, Juan D. Chavez, Xia Wu, Elizabeth Ramage, Pradeep K. Singh, Colin Manoil, James E. Bruce
Cell Chemical Biology, Volume 22, Issue 11, 19 November 2015, Pages 1521-1530 | doi:10.1016/j.chembiol.2015.09.015


HeLaNatureCommunications2015_BruceLab: Quantitative interactome analysis reveals a chemoresistant edgotype.
Juan D. Chavez, Devin K. Schweppe, Jimmy K. Eng, Chunxiang Zheng, Alex Taipale, Yiyi Zhang, Kohji Takara, James E. Bruce
Nature Communications, 6, Article number:7928 | doi:10.1038/ncomms8928


P.Aeruginosa_Structure2015: Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry.
Arti T. Navare, Juan D. Chavez, Chunxiang Zheng, Chad R. Weisbrod, Jimmy K. Eng, Richard Siehnel, Pradeep K. Singh, Colin Manoil, James E. Bruce
Structure, Volume 23, Issue 4, 7 April 2015, Pages 762-773 | doi:10.1016/j.str.2015.01.022


Weisbrodetal_JProteomeRes2013: In Vivo Protein Interaction Network Identified with a Novel Real-Time Cross-Linked Peptide Identification Strategy.
Chad R. Weisbrod, Juan D. Chavez, Jimmy K. Eng, Li Yang, Chunxiang Zheng, James E. Bruce
J. Proteome Res., 2013, 12 (4). | doi: 10.1021/pr3011638


Chavezetal_MolCellProteomics2013: Protein Interactions, Post-translational Modifications and Topologies in Human Cells.
Juan D. Chavez, Chad R. Weisbrod, Chunxiang Zheng, Jimmy K. Eng and James E. Bruce
Mol Cell Proteomics, 12, 1451-1467. | doi:10.1074/mcp.M112.024497


Ecoli2012_BingYang: Identification of cross-linked peptides from complex samples.
Bing Yang, Yan-Jie Wu, Ming Zhu, Sheng-Bo Fan, Jinzhong Lin, Kun Zhang, Shuang Li, Hao Chi, Yu-Xin Li, Hai-Feng Chen, Shu-Kun Luo, Yue-He Ding, Le-Heng Wang, Zhiqi Hao, Li-Yun Xiu, She Chen, Keqiong Ye, Si-Min He, Meng-Qiu Dong
Nature Methods, 9, 904-906 (2012) | doi:10.1038/nmeth.2099


Liu2015NatureMethods_Heck: Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry.
Fan Liu, Dirk T S Rijkers, Harm Post, Albert J R Heck
Nature Methods, 12, 1179-1184 (2015) | doi:10.1038/nmeth.3603


Leiker2015Ecoli_Lei: Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states
Dan Tan, Qiang Li, Mei-Jun Zhang, Chao Liu, Chengying Ma, Pan Zhang, Yue-He Ding, Sheng-Bo Fan, Li Tao, Bing Yang, Xiangke Li, Shoucai Ma, Junjie Liu, Boya Feng, Xiaohui Liu, Hong-Wei Wang, Si-Min He, Ning Gao, Keqiong Ye, Meng-Qiu Dong, Xiaoguang Lei
eLife 2016;5:e12509 | http://dx.doi.org/10.7554/eLife.12509


XLdb2013_Malmstrom: Cross-Link Guided Molecular Modeling with ROSETTA
Abdullah Kahraman , Franz Herzog , Alexander Leitner, George Rosenberger, Ruedi Aebersold, Lars Malmström
PLOS One Published: September 17, 2013 | http://dx.doi.org/10.1371/journal.pone.0073411


Kaake2014MCP_Huang: A New in Vivo Cross-linking Mass Spectrometry Platform to Define Protein–Protein Interactions in Living Cells
Robyn M. Kaake, Xiaorong Wang, Anthony Burke, Clinton Yu, Wynne Kandur, Yingying Yang, Eric J. Novtisky, Tonya Second, Jicheng Duan, Athit Kao, Shenheng Guan, Danielle Vellucci, Scott D. Rychnovsky, Lan Huang
MCP 13, 3533-3543 | http://dx.doi.org/10.1074/mcp.M114.042630