ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons

By F. Corpet, F. Servant, J. Gouzy, Daniel Kahn. Nucleic Acids Res., 2000

381 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

The Pfam protein families database (2004, methodology): “The Pfam-B families are derived from ProDom (4), a comprehensive set of protein domain families automatically generated from the Swiss-Prot and TrEMBL sequence databases.”
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins (2003, background): “There are now several globular protein domain databases accessible on the web, including Pfam (3), SMART (4), PROSITE (5), INTERPRO (6), PRODOM ( 7 ) and BLOCKS (8).”
The PredictProtein server (2003, neutral): “Kahn (Toulouse) (48) Pfam-A Protein families A.”
PRINTS and its automatic supplement, prePRINTS (2003, background): “1), which uses as input protein family clusters from ProDom (12).”
The InterPro database, an integrated documentation resource for protein families, domains and functional sites (2001, positive): “For example, sequence groups from ProDom are being analysed using the Pratt pattern discovery tool (11,12) to reveal clusters that can form InterPro families and to create regular expression discriminators.”
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families (2009, methodology): “The ProDom program [14] was used for alignment inspection and phylogenetic analysis.”
Identifying Protein Domains with the Pfam Database (2008, methodology): “The information on each clan is presented against annotation headings, as in Table 2.5.2, rather than in Stockholm format, with the family members of the clan being listed at the bottom against an MB ﬁeld-tag.”
The InterPro Database, 2003 brings increased coverage and new features (2003, methodology): “InterPro has developed an improved user interface for visualisation of the protein matches in a condensed graphical view derived from the ProDom graphical interface (4).”
Prototype selection for dissimilarity-based classifiers (2006, methodology): “A ProDom subset of 2604 protein domain sequences from the ProDom set [50] was selected by Roth [51].”
InterPro-an integrated documentation resource for protein families, domains and functional sites (2000, methodology): “, 2000), and BlastProDom for ProDom patterns (Corpet et al., 2000).”
The Pfam protein families database (2007, methodology): “In previous releases of Pfam, Pfam-B families were generated by taking clusters derived from MSP-crunch and latterly PRODOM (9) clusters, and removing regions covered by Pfam-A families to leave a set of Pfam-B clusters (10).”
The properties of protein family space depend on experimental design (2005, background): “ProDom).”
The Pfam protein families database (2011, methodology): “The Pfam-B families are derived from ProDom ( 4 ), a comprehensive set of protein domain families automatically generated from the Swiss-Prot and TrEMBL sequence databases.”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, background): “These tables also contain links to other sequence, structure and function annotation databases, such as PDB (4), GenBank (6), TrEMBL (5), CATH (42), Pfam (43) and ProDom (44).”
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 (2003, background): “This is an integrated resource of protein families, domains and sites which amalgamates the efforts of the member databases which are currently PROSITE (23), PRINTS (24), Pfam (25), ProDom (26), SMART (27) and TIGRFAMs (28).”