XWALK

Xwalk - Prediction, Validation and Visualisation of Chemical Cross-Links... So far, in protein structure prediction distance restraints from cross-linking experiments have been employed as an upper limit on the Euclidean distance between a pair of cross-linked amino acids. With Xwalk you can too use the Euclidean distance to validate your cross-link data. However, be aware that Euclidean distance is not a precise measure for deducing the cross-linkability between two amino acids. The Euclidean distance metric being a standard L 2 norm represents the length of the vector that connects two points (here any two atom centers of the cross-linked amino acids) in Cartesian space. However, such two points on the protein surface are likely separated by molecular slopes and depressions and form a physical barrier for a cross-linker molecule. The cross-linker molecule cannot penetrate these barriers but must circumvent them to bridge two reactive amino acids covalently together. Thus, a more..

Primary location: Muttenz Switzerland