Extract one monomer from each of the two multimers. Align the binding sites (via the 'Align Binding Sites' node) or the whole structure (using the 'Protein Structure Alignment' node).
Get this workflow from the following link: Download
Protein Alignment consists of the following 22 nodes(s):
Protein Alignment contains nodes provided by the following 3 plugin(s):
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Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.