Xlink Analyzer specifications

Information


Unique identifier OMICS_08033
Name Xlink Analyzer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jan Kosinski <>

Publication for Xlink Analyzer

Xlink Analyzer in publications

 (6)
PMCID: 5789952
PMID: 29317535
DOI: 10.1073/pnas.1718426115

[…] for lc-based ms measurements. data processing was performed using xquest/xprophet. identified cross-links were mapped onto the saxs model of the stat2133–679/irf9–iad heterodimer and analyzed using xlink analyzer ()., proteins were extensively dialyzed against itc buffer [20 mm hepes (ph 7.5), 300 mm nacl, 2% glycerol] and subjected to calorimetry using a microcal itc200 system (malvern […]

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

[…] 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 in an approximately fivefold molar excess over bait nups or bait nup complexes immobilized via prota, gst, or flag tags in the presence of e. coli […]

PMCID: 5105147
PMID: 27824037
DOI: 10.1038/ncomms13248

[…] score=0.95, ms1 tolerance window±3 p.p.m. the reliability of the identified inter-protein cross-links was ultimately assessed in the context of available x-ray structures or homology models using xlink analyzer (). for these analyses, an additional conservative cut-off of ld score≥30 was applied within xlink analyzer., an in silico homology model of the 30s subunit from s. solfataricus […]

PMCID: 4712189
PMID: 26711008
DOI: 10.1016/j.molcel.2015.11.016

[…] velos pro instrument (thermo scientific). mass spectrometry data were processed using the xquest/xprophet. identified crosslinks were mapped to known polymerase structures and analyzed using xlink analyzer ()., e.t., supervised by d.h., expressed and crystallized the h5n1 pb2-c and solved the structure with the help of a.p. d.g. crystallized flub polymerase with c5′ or v5′ rna; performed […]

PMCID: 4681132
PMID: 26605533
DOI: 10.1038/nature16143

[…] placed into the elongating pol iii map by rigid body fitting. the fitted structures of individual subunits were used to aid de novo model building and re-building of reference models. additionally, xlink analyzer was used to display available lysine-lysine crosslinks and photo-crosslinks on the pol iii model, which allowed us to assign several peripheral densities to subunits c31, c34, c37 […]


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Xlink Analyzer institution(s)
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
Xlink Analyzer funding source(s)
The work was supported by the EMBL Interdisciplinary Postdoc Programme under Marie Curie COFUND Actions (J.K.), an Advanced Grant of the European Research Council (ERC-2013-AdG340964-POL1PIC) to C.W.M.

Xlink Analyzer review

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Anonymous user #1803

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Desktop
very useful- thanks!