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Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.

Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M - J. Struct. Biol. (2015)

Bottom Line: Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques.To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures.We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

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Overview of Xlink Analyzer functionality.
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f0005: Overview of Xlink Analyzer functionality.

Mentions: To enable the interactive and comprehensive analysis of XL-MS data within a sophisticated 3D molecular viewer and structural analysis tool that is widely used in the structural biology community, such as UCSF Chimera (Pettersen et al., 2004), we developed the Xlink Analyzer plugin. Xlink Analyzer is an interactive graphical software. It is seamlessly integrated within UCSF Chimera and allows importing mass spectrometry data, displaying cross-links in the context of structures, automatically detecting violated cross-links, calculating the number of satisfied and violated cross-links, and plotting distributions of distances between cross-linked residues (Fig. 1). It includes tools for filtering the cross-links by confidence score, locating and displaying subsets of cross-links (e.g. inter-links, intra-links or cross-links connecting particular subunits), mapping positions of mono-links, and comparing different cross-linking datasets. Xlink Analyzer also provides an interface for coloring, selecting, hiding or displaying individual subunits or subcomplexes, which, as compared to capabilities of standard Chimera structure operation tools, greatly facilitates analysis of very large complexes (Fig. A.1E). Xlink Analyzer is freely available as open-source software.


Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.

Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M - J. Struct. Biol. (2015)

Overview of Xlink Analyzer functionality.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4359615&req=5

f0005: Overview of Xlink Analyzer functionality.
Mentions: To enable the interactive and comprehensive analysis of XL-MS data within a sophisticated 3D molecular viewer and structural analysis tool that is widely used in the structural biology community, such as UCSF Chimera (Pettersen et al., 2004), we developed the Xlink Analyzer plugin. Xlink Analyzer is an interactive graphical software. It is seamlessly integrated within UCSF Chimera and allows importing mass spectrometry data, displaying cross-links in the context of structures, automatically detecting violated cross-links, calculating the number of satisfied and violated cross-links, and plotting distributions of distances between cross-linked residues (Fig. 1). It includes tools for filtering the cross-links by confidence score, locating and displaying subsets of cross-links (e.g. inter-links, intra-links or cross-links connecting particular subunits), mapping positions of mono-links, and comparing different cross-linking datasets. Xlink Analyzer also provides an interface for coloring, selecting, hiding or displaying individual subunits or subcomplexes, which, as compared to capabilities of standard Chimera structure operation tools, greatly facilitates analysis of very large complexes (Fig. A.1E). Xlink Analyzer is freely available as open-source software.

Bottom Line: Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques.To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures.We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.

No MeSH data available.


Related in: MedlinePlus