SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments

By Julian Gough, Cyrus Chothia. Nucleic Acids Res., 2002

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Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains (2016, methodology): “For example, the tool SuperFamily only uses seeds with solved structure, while Pfam starts with any recognizable domain.(34,35) Tools also differ in the curation of the profiles obtained, with Pfam using human intervention to group structurally related families into clans.”
EVA: evaluation of protein structure prediction servers (2003, background): “Superfamily http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ J Gough ( 36 ) Inter-residue contacts CORNET http://prion.biocomp.unibo.it/cornet.html P Fariselli, O Olmea and A Valencia, R Casadio (10,37,38) PDGCON http://www.pdg.cnb.uam.es:8081/ F Pazos, O Olmea and A Valencia (13) CONcons/CONhydro http:”
IL-33, an interleukin-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines. (2005, methodology): “…of dog DVS-27 (Onda et al., 1999) (accession # BAA75891) was identiﬁed by this effort from GenBank, and its IL-1 family assignment was secured by Superfamily (Gough and Chothia, 2002) and 3D-PSSM (Kelley et al., 2000) fold recognition methods that matched ittoIL-1/FGF b -trefoilfold templates.”