SMART 4.0: towards genomic data integration

By Ivica Letunic, Richard R. Copley, Steffen Schmidt, F. Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, Peer Bork. Nucleic Acids Res., 2004

1,041 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/08c098c4f3f890c97afcef8ab7402bcaca05653f

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Citations in the corpus

Genome-Wide Comparative Analysis and Expression Pattern of TCP Gene Families in Arabidopsis thaliana and Oryza sativa (2007, neutral): “(http://smart.embl-heidelberg.de/; Schultz et al. 1998; Letunic et al. 2004).”
CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo (2013, methodology): “Cloning and expression of mouse B-ZIP proteins The DNA binding domain (DBD) of B-ZIPs as defined in the Pfam (Finn et al. 2008) and SMART (Letunic et al. 2004) database (Supplemental Table 7) were cloned into the pETGEXCT (C-terminal GST) vector (Sharrocks 1994) either by RT-PCR from pooled mouse…”
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”
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines (2004, neutral): “All domains are cross-referenced back to their parent protein databases [Swiss-Prot + TrEMBL (4), PIR (5) and to entries in other domain repositories, such as INTERPRO (6), or its member databases such as Pfam (7), SMART (8) and PRINTS (9)].”
Pfam: clans, web tools and services (2005, background): “black domain is the ACR domain from SMART (15).”
CDD: a Conserved Domain Database for protein classification (2004, methodology): “CDD also contains models from SMART, and several hundred NCBI-curated domain models, identiﬁable by accessions starting with ‘cd’.”
The SET-domain protein superfamily: protein lysine methyltransferases (2005, background): “There are currently 157 entries for human SET-domain proteins in the SMART database [11] and 93 entries in the Pfam database [12], although both databases contain duplicate entries.”
eggNOG: automated construction and annotation of orthologous groups of genes (2007, neutral): “These annotations are produced by a pipeline, which summarizes the available functional information on the proteins in each cluster: (1) the textual annotation for these proteins, (2) their annotated Gene Ontology (GO) terms (14), (3) their membership to KEGG pathways (15) and (4) the presence of pr”
The ProDom database of protein domain families: more emphasis on 3D (2004, background): “This comprehensiveness makes ProDom a unique resource usefully complementing expert derived databases, such as PROSITE (4), PFAM (5) or SMART (6), thereby helping to sustain the rapid growth of InterPro (7,8).”
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).”
DOG 1.0: illustrator of protein domain structures (2009, neutral): “For example, the Pfam [1], SMART [2], PROSITE [3], InterPro [4] and other related databases or online tools could predict the functional domain organization of a given protein sequence, and generate the result into a figure.”
TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes (2005, methodology): “The automatically assigned domains, which are linked to the corresponding Pfam, SMART and PROSITE entries, are meant to complement the manually annotated domains, many of which are based on functional studies reported in the original literature.”
The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode (2005, methodology): “cgi) and the SMART system [174], and indepth, iterative database searches were performed using the PSI-BLAST program [175].”
SMART 5: domains in the context of genomes and networks (2005, background): “55 system (RDBMS) which stores information on SMART domains (1,12).”
CD-Search: protein domain annotations on the fly (2004, methodology): “We thank the architects of the Pfam, SMART and COGs collections and the curators of the CDD for their invaluable contributions.”