The Pfam protein families database

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ProGen: Language Modeling for Protein Generation (2020, methodology): “We curate the protein sequences and associated tags available in Uniparc [24], UniprotKB [7], SWISS-PROT [6], TrEMBL [10], Pfam [8], and NCBI taxonomic information [16].”
Marine DNA viral macro- and micro-diversity from pole to pole (2019, methodology): “, 2015), searching for matches against the InterPro protein signature database using InterProScan (Zdobnov and Apweiler, 2001), and running HMM searches against Pfams (Bateman et al., 2004).”
Clustering of database sequences for fast homology search using upper bounds on alignment score. (2004, methodology): “Thus, the proposed method might be applicable to the family detection based on profiles of protein families such as HMM [3].”
PIRSF: family classification system at the Protein Information Resource (2004, background): “For example, Pfam-based searches can identify all PIRSFs sharing one or more Pfam domains (12).”
A reference genome for common bean and genome-wide analysis of dual domestications (2014, methodology): “Finn, R.D. et al. The Pfam protein families database.”