In a recent issue of Nature Protocols, Orbán-Németh et al.1 present a protocol to predict structural models of proteins and their complexes from mass spectrometry (MS) cross-linking data. We read the protocol with interest, as it uses third-party software including the HADDOCK web portal2 that we developed and maintain. While we endorse and encourage the inclusion of our software in other protocols and pipelines, it is important that its usage be accurately and correctly described to avoid problems and incorrect results that we, as primary developers, will have to troubleshoot.

doi: https://doi.org/10.1038/s41596-018-0017-6