General Information
| Description | Computing and visualizing distances in cross-linking experiments |
| Homepage | http://www.xwalk.org |
Publications
Xwalk: computing and visualizing distances in cross-linking experiments
Motivation:
Chemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology.
Results:
Here, we introduce the algorithm Xwalk for predicting and validating these cross-links on existing protein structures. Xwalk calculates and displays non-linear distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules. It returns a ‘solvent accessible surface distance’, which corresponds to the length of the shortest path between two amino acids, where the path leads through solvent occupied space without penetrating the protein surface.
Availability:
Xwalk is freely available as a web server or stand-alone JAVA application at http://www.xwalk.org.
Contact:
abdullah@imsb.biol.ethz.ch; aebersold@imsb.biol.ethz.ch
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
SQID-XLink
Published July 2012
Implementation of an intensity-incorporated algorithm for cross-linked peptide identification
XLmap
Published September 2015
An R package to visualize and score protein structure models based on sites of protein cross-linking
PseKRAAC
Published August 2016
A flexible web server for generating pseudo K-tuple reduced amino acids composition
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