SMART 5: domains in the context of genomes and networks

By Ivica Letunic, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork. Nucleic Acids Res., 2005

987 citations recorded by the source corpus.

The Simple Modular Architecture Research Tool (SMART) is an online resource () used for protein domain identification and the analysis of protein domain architectures. Many new features were implemented to make SMART more accessible to scientists from different fields. The new ‘Genomic’ mode in SMART makes it easy to analyze domain architectures in completely sequenced genomes. Domain annotation has been updated with a detailed taxonomic breakdown and a prediction of the catalytic activity for 50 SMART domains is now available, based on the presence of essential amino acids. Furthermore, intrinsically disordered protein regions can be identified and displayed. The network context is now displayed in the results page for more than 350 000 proteins, enabling easy analyses of domain interactions.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b0e8dd9d493d4cf814ec565a8c956d63c32d52b7

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Citations in the corpus

The Ensembl gene annotation system (2016, methodology): “We identify these signatures by both ab initio sequence search [SEG (95), SignalP (96), ncoils (97), TMHMM (98)] and searching protein domain databases for sequence matches [PRINTS (99), Pfscan (100), Pfam (101), TIGRFAM, SUPERFAMILY (102), SMART (103) and PIRSF (104)].”
SMART 6: recent updates and new developments (2008, methodology): “Here we summarize the major changes and new features that have been introduced since our last report (2).”
Pseudo Amino Acid Composition and its Applications in Bioinformatics, Proteomics and System Biology (2009, methodology): “Based on such a fact, several FunD databases were developed, such as SMART [180], Pfam [181], COG [182], KOG [182], CDD [183].”
A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data (2008, methodology): “The created Hidden-Markov-Models are incorporate into domain search web service SMART [37].”
A New Method for Predicting the Subcellular Localization of Eukaryotic Proteins with Both Single and Multiple Sites: Euk-mPLoc 2.0 (2010, neutral): “Of these databases, CDD contains the domains imported from COG, Pfam and SMART, and hence is relatively much more complete [57].”
Some remarks on protein attribute prediction and pseudo amino acid composition (2010, background): “Since then, a series of new protein FunD databases were established, such as COG (Tatusov et al., 2003), KOG (Tatusov et al., 2003), SMART (Letunic et al., 2006), Pfam (Finn et al., 2006), and CDD (Marchler-Bauer et al., 2007).”
Recent developments in the MAFFT multiple sequence alignment program (2008, background): “In such a situation, the use of databases of annotated alignments [ 107 , 108] will be a fruitful and practical way to construct an accurate MSA, as well as to extract solid information from an MSA [109].”
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins (2006, methodology): “The graphical view is a symbolic representation of matches, inspired by SMART (11) and predicted features in a high quality image (Portable Network Graphics format) that can be used in presentations or papers (Figure 1).”
Improved human disease candidate gene prioritization using mouse phenotype (2007, background): “[41], Pfam [42], SMART [43], PROSITE [44], Gene3D [45] and ProDom [46].”
SMART 7: recent updates to the protein domain annotation resource (2011, methodology): “(1) an initial list of proteins is obtained through an architecture analysis query; (2) proteins are grouped according to their species of origin; (3) these species are used to ‘prune’ the complete NCBI taxonomy database (12) by walking the taxonomy tree up to the root and exporting the resulting st”
Database resources of the National Center for Biotechnology Information (2009, methodology): “The CDD (48) contains over 28 000 PSI-BLASTderived Position Specific Score Matrices representing domains taken from the Simple Modular Architecture Research Tool (Smart) (52), Pfam (53), TIGRFAM (54) and from domain alignments derived from COGs and Entrez Protein Clusters.”
Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization (2010, background): “Of these databases, CDD contains the domains imported from COG, Pfam, and SMART, and hence is relatively much more complete [38] and will be adopted in this study.”
Database resources of the National Center for Biotechnology Information (2014, methodology): “CDD (45) contains PSI-BLAST-derived Position Specific Score Matrices representing domains taken from the Simple Modular Architecture Research Tool (Smart) (46), Pfam (47), TIGRFAM (48) and from domain alignments derived from the Clusters of Orthologous Groups (COGs) database and the Protein Clusters”
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine (2007, methodology): “The Evidence page also provides options for querying the input transcript against well-annotated database, such as the functional domain database Pfam (29), SMART (30) and SuperFamily (31), UTRdb (32) and ncRNA database RNAdb (27).”
Database resources of the National Center for Biotechnology Information: update (2004, methodology): “Score Matrices representing domains taken from the Simple Modular Architecture Research Tool (Smart) (46) , Pfam (47) , TIGRFAM (48) and from domain alignments derived from the Clusters of Orthologous Groups (COGs) database and the Protein Clusters database.”