CLAUDIO: Automated Structural Analysis of Cross-Linking Data

Motivation Cross-linking mass spectrometry has made remarkable advancements in the high-throughput characterization of protein structures and interactions. The resulting pairs of cross-linked peptides typically require geometric assessment and validation, given the availability of their corresponding structures.Results CLAUDIO (Cross-linking Analysis Using Distances and Overlaps) is an open-source software tool designed for the automated analysis and validation of different varieties of large-scale cross-linking experiments. Many of the otherwise manual processes for structural validation (i.e. structure retrieval and mapping) are performed fully automatically to simplify and accelerate the data interpretation process. In addition, CLAUDIO has the ability to remap intra-protein links as inter-protein links and discover evidence for homo-multimers.Availability and implementation CLAUDIO is available as open-source software under the MIT license at https://github.com/KohlbacherLab/CLAUDIO.