Given a set of protein sequences (in fasta format), InterPreTS will use BLAST to find homologues of known structure for all pairs (i.e. templates that can model each pair of sequences based on homology) and then evaluate the suitability of those templates for modelling the interaction
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Aloy P, Russell RB.
InterPreTS: protein interaction prediction through tertiary structure.
Bioinformatics. 2003 Jan;19(1):161-2.