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xiNET specifications

Information


Unique identifier OMICS_08035
Name xiNET
Interface Web user interface
Restrictions to use None
License Apache License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Juri Rappsilber <>

Publication for xiNET

xiNET in publications

 (11)
PMCID: 5795388
PMID: 29222160
DOI: 10.1074/mcp.RA117.000470

[…] to calculate alternative interaction spaces with the disvis web server (), assuming a maximum cross-linked cα–cα distance of 30 å., interaction networks were generated using cytoscape v3.4 () and xinet ()., blue native page sample and gel running buffers and native unstained molecular weight marker were obtained commercially (thermo fisher scientific). mitochondria were resuspended in 1x […]

PMCID: 5755487
PMID: 29286378
DOI: 10.3791/56747

[…] reagents, peak pairs in ms spectra can be used as an additional quality control., if required, visualize the cross-linking results in protein interaction networks using software tools (e.g., xvis, xinet). use bar plots or circular plots for visualization of protein interactions. note: both software tools are freely available on a web server. follow detailed instructions on the respective […]

PMCID: 5653651
PMID: 29062044
DOI: 10.1038/s41467-017-01160-9

[…] table ), in line with previous xl-ms analyses of known protein structures, . the entire data set containing all crosslinks regardless of their ld-score is shown in supplementary data . the xinet crosslink viewer was used to create the crosslink map shown in fig. . the crosslinks were mapped to the model and analyzed using xlink analyzer., purified prey nups were added […]

PMCID: 5501727
PMID: 28648606
DOI: 10.1016/j.str.2017.05.016

[…] search results were filtered according to a ms1 mass tolerance window –3 to 7 ppm and finally each ms/ms spectra was manually inspected and validated. cross-link network maps were created with xinet ()., the structures determined by cryo-em have been deposited in the emdb with accession codes emd-3677 and emd-3678, for yeast rvb1p-rvb2p and yeast r2tp respectively., a.r.-c., m.p., c.p., […]

PMCID: 5467213
PMID: 28585565
DOI: 10.1038/ncomms15741

[…] (2) the max score value from each data set was higher than 5; (3) each crosslink must have a minimal spectral count of 2 in each data set. the final result was subsequently visualized using the xinet online server. the same strategy was used for paf1c xl-ms, except that the samples were measured on an ab sciex triple-tof instrument (ab sciex)., to reconstitute a homogeneous pol […]


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xiNET institution(s)
Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK

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