The ProDom database of protein domain families: more emphasis on 3D

By C. Bru, Emmanuel Courcelle, S. Carrère, Yoann Beausse, Sandrine Dalmar, Daniel Kahn. Nucleic Acids Res., 2004

350 citations recorded by the source corpus.

ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/46e2fd3c64ac2dbf725c05b5e7a49678163ff97b

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Citations in the corpus

New developments in the InterPro database (2007, methodology): “Reference InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER.”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, neutral): “The InterPro consortium integrates databases of protein families, domains and functional sites, including: Gene3D (30), PANTHER (31), Pfam (32), PIRSF (33), PRINTS (34), ProDom (35), PROSITE (36), SMART (37), SUPERFAMILY and TIGRFAMs (38).”
The InterPro protein families database: the classification resource after 15 years (2014, background): “As can be seen, the level of integrated entries is in excess of 90% for all databases, except CATH-Gene3D, Superfamily, PAN-THER and ProDom.”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, background): “The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families Shibu Yooseph 1* , Granger Sutton 1 , Douglas B. Rusch 1 , Aaron L. Halpern 1 , Shannon J. Williamson 1 , Karin Remington 1 ,”
Pfam 10 years on: 10 000 families and still growing (2008, background): “However, there is a supplementary set of Pfam families called Pfam-B that are automatically generated from the ProDom database of protein domain families [6].”
InterProScan 5: genome-scale protein function classification (2014, methodology): “As InterProScan 5 makes use of the Hibernate object-relational mapping tool (http://www.hibernate.org/), it should be possible to port the back-end to run on most relational database management systems.”
InterProScan: protein domains identifier (2005, background): “ProDom ( 6 ) BlastProDom (Blastall) (4) PRINTS (7) FingerPrintScan (8) SMART (9) Hmmpfam (http://hmmer.wustl.edu/) TIGRFAMs (10) Hmmpfam (http://hmmer.wustl.edu/) Pfam (11) Hmmpfam (http://hmmer.wustl.edu/) PROSITE (12) ScanRegExp + ProfileScan (13) PIRSF (14) Hmmpfam (http://hmmer.wustl.edu/) SUPER”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “Launched in 1999, InterPro is derived from 14 different specialist member databases: CATH-Gene3D (2), the Conserved Do-mains Database (CDD) (3), HAMAP (4), PANTHER (5), Pfam (6), PIRSF (7), PRINTS (8), ProDom (9), PROSITE Patterns (10), PROSITE Profiles (10), SMART (11), the Structure–Function Linka”
InterPro in 2011: new developments in the family and domain prediction database (2011, methodology): “The InterPro database integrates predictive models, or signatures, from multiple, diverse source repositories: Pfam (1), PRINTS (2), PROSITE (3), SMART (4), ProDom (5), PIRSF (6), SUPERFAMILY (7), PANTHER (8), CATHGene3D (9), TIGRFAMs (10) and HAMAP (11).”
The InterPro protein families and domains database: 20 years on (2020, background): “ProDom is a database of protein domain families based on the automatic clustering of sequences by similarity (21).”
Improved human disease candidate gene prioritization using mouse phenotype (2007, background): “[41], Pfam [42], SMART [43], PROSITE [44], Gene3D [45] and ProDom [46].”