Xwalk
Description
Chemical cross-linking of proteins or protein complexes and the mass spectrometry based localization of the cross-linked amino acids is a powerful method for generating distance restraints on the substrate’s topology. Xwalk was written to predict and validate 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.
Environment Modules
Run module spider xwalk to find out what environment modules are available for this application.
System Variables
- HPC_XWALK_DIR - installation directory
Citation
If you publish research that uses xwalk you have to cite it as follows:
Kahraman A., Malmström L., Aebersold R. (2011). Xwalk: Computing and Visualizing Distances in Cross-linking Experiments. Bioinformatics, doi:10.1093/bioinformatics/btr348.