Abstract Motivation Chemical cross-linking combined with mass spectrometry (CXMS) is now a well-established method for profiling existing protein–protein interactions (PPIs) with partially known structures. It is expected to map the results of CXMS with existing structure databases to study the protein dynamic profile in the structure analysis. However, currently available structure-based analysis software suffers from the difficulty of achieving large-scale analysis. Besides, it is infeasible for structure analys…