DynamXL provides a means to compare experimental cross-linking data against protein structural information.
DynamXL accounts for the ﬂexible nature of both protein and cross-linker molecules by (1) predicting the accessible space of amino acid side chains, (2) aggregating measures from multiple protein conformations and (3) measuring distances with a powerful shortest path algorithm, Theta*. The software, developed in Python, can be controlled via a graphical user interface, via terminal, or directly imported into an external code.
DynamXL has been developed by Matteo while in the Benesch group, at the University of Oxford.
Software and user manual are freely available for academia here
When using DynamXL in your work, please cite:
Degiacomi, M.T. ✉, Schmidt, C. , Baldwin, A.J., Benesch, J.L.P. (2017). Accommodating Protein Dynamics in the Modeling of Chemical Crosslinks, Structure, 25(11), 1751-1757.