SMART 4.0: towards genomic data integration. SMART (Simple Modular Architecture Research Tool) is a web tool ( for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins. The January 2004 release of SMART contains 685 protein domains. New developments in SMART are centred on the integration of data from completed metazoan genomes. SMART now uses predicted proteins from complete genomes in its source sequence databases, and integrates these with predictions of orthology. New visualization tools have been developed to allow analysis of gene intron–exon structure within the context of protein domain structure, and to align these displays to provide schematic comparisons of orthologous genes, or multiple transcripts from the same gene. Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries.

References in zbMATH (referenced in 16 articles , 1 standard article )

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  1. Rout, Subhashree; Mahapatra, Rajani Kanta: \textitInsilico analysis of \textitplasmodiumfalciparum CDPK5 protein through molecular modeling, docking and dynamics (2019)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  3. Chou, Kuo-Chen: Some remarks on protein attribute prediction and pseudo amino acid composition (2011)
  4. Shen, Hong-Bin; Chou, Kuo-Chen: Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins (2010)
  5. Pettifer, Steve; Thorne, David; Mcdermott, Philip; Marsh, James; Villéger, Alice; Kell, Douglas B.; Attwood, Teresa K.: Visualising biological data: a semantic approach to tool and database integration (2009) ioport
  6. Rendon, Gloria; Ger, Mao-Feng; Kantorovitz, Ruth; Natarajan, Shreedhar; Tilson, Jeffrey; Jakobsson, Eric: Understanding the “horizontal dimension” of molecular evolution to annotate, classify, and discover proteins with functional domains (2009) ioport
  7. Shen, Hong-Bin; Chou, Kuo-Chen: Predicting protein fold pattern with functional domain and sequential evolution information (2009)
  8. Via, Allegra; Gould, Cathryn M.; Gemünd, Christine; Gibson, Toby J.; Helmer-Citterich, Manuela: A structure filter for the eukaryotic linear motif resource (2009) ioport
  9. Bernardes, Juliana S.; Davila, Alberto Mr; Costa, Vitor S.; Zaverucha, Gerson: Improving model construction of profile hmms for remote homology detection through structural alignment (2007) ioport
  10. Mistry, Jaina; Bateman, Alex; Finn, Robert D.: Predicting active site residue annotations in the pfam database (2007) ioport
  11. Xia, Xuhua: Bioinformatics and the cell. Modern computational approaches in genomics, proteomics and transcriptomics (2007)
  12. Letunic, Ivica; Copley, Richard R.; Pils, Birgit; Pinkert, Stefan; Schultz, Jörg; Bork, Peer: SMART 5: Domains in the context of genomes and networks. (2006) ioport
  13. Portugaly, Elon; Harel, Amir; Linial, Nathan; Linial, Michal: EVEREST: Automatic identification and classification of protein domains in all protein sequences (2006) ioport
  14. Zhu, Tao; Zhou, Jianfeng; An, Yuming; Zhou, Jinhua; Li, Hongyu; Xu, Gang; Ma, Ding: Construction and characterization of a rock-cluster-based EST analysis pipeline (2006)
  15. Letunic, Ivica; Copley, Richard R.; Schmidt, Steffen; Ciccarelli, Francesca; Doerks, Tobias; Schultz, Jörg; Ponting, Chris P.; Bork, Peer: SMART 4.0: Towards genomic data integration. (2004) ioport
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