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.