Xwalk

The software tool Xwalk is designed to predict and validate chemical cross-links of proteins or protein complexes using mass spectrometry-based localization of cross-linked amino acids in peptide sequences. Xwalk calculates non-linear distances between cross-linked amino acids on protein surfaces, taking into account 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.

Topic

Small molecules;Protein structural motifs and surfaces;Protein folds and structural domains;Structure prediction;Proteins

Detail

  • Operation: Protein model validation;Accessible surface calculation;Molecular surface calculation;Protein property calculation;Residue distance calculation

  • Software interface: Web user interface

  • Language: Javascript;Java

  • License: Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)

  • Cost: Free

  • Version name: -

  • Credit: ETH Zurich; the Commission of the European Communities through the PROSPECTS consortium, SystemsX.ch – The Swiss Initiative for Systems Biology.

  • Input: -

  • Output: -

  • Contact: Abdullah Kahraman abdullah@imsb.biol.ethz.ch

  • Collection: -

  • Maturity: -

Publications

  • Xwalk: computing and visualizing distances in cross-linking experiments.
  • Kahraman A, et al. Xwalk: computing and visualizing distances in cross-linking experiments. Xwalk: computing and visualizing distances in cross-linking experiments. 2011; 27:2163-4. doi: 10.1093/bioinformatics/btr348
  • https://doi.org/10.1093/bioinformatics/btr348
  • PMID: 21666267
  • PMC: PMC3137222

Download and documentation

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