Pfam: A comprehensive database of protein domain families based on seed alignments

By Erik L. L. Sonnhammer, Sean R. Eddy, Richard Durbin. 1997

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Citations in the corpus

The Pfam protein families database (2011, background): “Pfam is designed to be a comprehensive and accurate collection of protein domains and families ( 1 ,2).”
Role for a bidentate ribonuclease in the initiation step of RNA interference (2001, background): “In addition to RNase III and helicase motifs, searches of the PFAM database indicate that each Dicer family member also contains a PAZ domain (see Supplementary Information”
Identifying Protein Domains with the Pfam Database (2008, background): “Pfam is a database of such protein domain families (Sonnhammer et al., 1997 ; Finn et al ., 2008 ) , with each family represented by a multiple sequence alignment and a proﬁle hidden Markov model (HMMs; see APPENDIX 3A ).”
A gene expression atlas of the model legume Medicago truncatula. (2008, methodology): “…DNA-binding domains, using InterPro (http://www.ebi.ac.uk/interpro/) and Pfam (http://pfam.sanger.ac.uk/) domain identification, additional hidden Markov model (HMM) predictions (Guo et al., 2005; Sonnhammer et al., 1997), and a BLASTX search of the NCBI NR database to support annotations.”
Structural basis for loading and inhibition of a bacterial T6SS phospholipase effector by the VgrG spike (2020, methodology): “Protein domains were identified using Pfam (Sonnhammer et al , 1997) or CDart (Geer et al , 2002).”
MobiDB‐lite: fast and highly specific consensus prediction of intrinsic disorder in proteins (2017, methodology): “The annotation of proteomes from sequence has been dominated by the concept of protein domains for a long time (Lee et al., 2005; Sonnhammer et al., 1997).”
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences (2007, methodology): “The number of proteins and individual repeats detected confidently by TPRpred, Pfam and SMART are tabulated in Table 3.”
GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank (2017, methodology): “2) domains and motifs: they are usually functional sites of a query protein, and all of them in the query sequence are detected by using protein domain/motif resources, such as CATH [7], SCOP [22] and Pfam [28], to understand the function of the query protein.”
Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009308. (2003, methodology): “Individual repeats within the LRR were recognized inefficiently by protein domain analysis programs such as hmmpfam and hmmsearch (Sonnhammer et al., 1997) and SMART (Schultz et al.”
Discovering common stem-loop motifs in unaligned RNA sequences. (2001, background): “They are related to hidden Markov models, which are now commonly used to represent protein families (24,25), except that they also capture the constraints of the base pairs in the RNA structure.”
mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. (2002, unknown): “6 fragment Brunn, G.J., Williams, J., Sabers, C., Wiederrecht, G., Lawrence, search (Sonnhammer et al., 1997) at http://pfam.wustl.edu.”
HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. (2000, background): “Previous applications of HMMs to biological sequence data include the problems of ®nding coding regions in DNA and splice junctions (Kulp et al., 1996, Burge & Karlin, 1998, Lukashin & Borodovsky, 1998, Henderson et al., 1997), ®nding transmembrane regions in proteins (Sonnhammer et al., 1998), and ”
DAVID: Database for Annotation, Visualization, and Integrated Discovery (2003, background): “DomainCharts display the distribution of differentially expressed genes among PFAM protein domains [14].”