ProDom: Automated Clustering of Homologous Domains

By F. Servant, C. Bru, S. Carrère, Emmanuel Courcelle, J. Gouzy, David Peyruc, Daniel Kahn. Briefings Bioinform., 2002

372 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/bd1ed06fc70dd10cf650e7cb0e760108aa62e94e

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In Molecular Biology

Citations in the corpus

UniProt: the Universal Protein knowledgebase (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs (18).”
ModBase, a database of annotated comparative protein structure models and associated resources (2013, background): “These tables also contain links to other sequence, structure and function annotation databases, such as PDB (4), GenBank (3), Swiss-Prot/TrEMBL (2), CATH (32), Pfam (33), ProDom ( 34 ), and UCSC Genome Browser (35).”
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems (2014, methodology): “The components of the systems are searched using protein profiles encoded as hidden Markov models (HMM), such as those available in databases like PFAM, TIGRFAM or PRODOM [10–12].”
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 (3), Swiss-Prot/TrEMBL (2), CATH (32), Pfam (33), ProDom (34), and UCSC Genome Browser (35).”
Tools for comparative protein structure modeling and analysis (2003, background): “These tables also contain links to other sequence, structure and function annotation databases, such as PDB (3), GenBank (28), SWISS-PROT (2), CATH (29), PFAM (30) and PRODOM (31).”
The Universal Protein Resource (UniProt) (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (14), PROSITE (15), PRINTS (16), ProDom (17), SMART (18), PIRSF (19), Superfamily (20) and TIGRFAMs (21).”
ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins (2003, methodology): “Connections to ESPript are now available from the protein domain database ProDom (14), the structure prediction server PredictProtein (15) and the server performing sequence analysis and similarities searches NPS@ (16).”
GlobPlot: exploring protein sequences for globularity and disorder (2003, methodology): “There are many methods, such as SMART (Simple Modular Architecture Research Tool) (3), PRODOM (4) , Pfam (5,6), PROSITE (7) and ELM (Eukaryotic Linear Motif, http:// elm.eu.org) (8), available for finding globular domains (e.g. SH3, TyrKc, active sites) and linear motifs (e.g. SH3 ligands, LXXLL nuc”
Empirical comparison of ab initio repeat finding programs (2008, methodology): “One means by which large consensus sequence libraries could be reduced to a manageable size would be to follow ab initio repeat identification with domain identification using systems such as MOSAIC (30), ProDom (31), Domain Organizer (32) and/or the A-bruijn approach (27).”
The ProDom database of protein domain families: more emphasis on 3D (2004, methodology): “11 databases, essentially as described previously (2,7).”
InterPro, progress and status in 2005 (2004, methodology): “InterPro (1) integrates into one resource the major protein signatures databases: PROSITE (2), which uses regular expressions and profiles, PRINTS (3), which uses position-specific scoring matrix-based (PSSM-based) fingerprints, ProDom (4), which uses automatic sequence clustering, and Pfam (5), SMA”
Ortholog identification in the presence of domain architecture rearrangement (2011, methodology): “The Berkeley PhyloFacts Orthology Group (PHOG) [55] algorithm makes use of both tree topology and tree edge lengths to identify orthologs based on gene trees in the PhyloFacts Phylogenomic Encyclopedia [11]; a tree-distance threshold allows biologists control over the precision–recall trade-off and ”
Enzyme-specific profiles for genome annotation: PRIAM. (2003, background): “Because enzyme collections are usually relatively small sequence sets, the resulting modules are not necessarily decomposed into individual domains: they tend to be longer than domains as deﬁned in ProDom (14), Pfam (15) or SCOP (16).”
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks (2008, background): “Protein sequence pages (associated with a Gene page) are, in turn, additionally linked to records from GenPept (14), InterPro (37), PRINTS (38), PROSITE (39), ProDom (40), SMART (41), Pfam (42) and, when appropriate, to a species-specific gene page in FlyBase (43) or ZFIN (44).”