1 Xwalk: Computing and Visualizing Distances in Cross-linking Ex- periments

Motivation: Chemical cross-linking of proteins or protein complexes and the mass spectrometry based localization of the cross-linked amino acids in the peptide sequences is a powerful method for gen-erating 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 pro-tein surface. Availability: Xwalk is freely available as a webserver or standalon