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Nucleic Acids Research, 2002, Vol. 30, No. 1 242-244
© 2002 Oxford University Press

Recent improvements to the SMART domain-based sequence annotation resource

Ivica Letunic, Leo Goodstadt1, Nicholas J. Dickens1, Tobias Doerks, Joerg Schultz, Richard Mott2, Francesca Ciccarelli, Richard R. Copley, Chris P. Ponting1 and Peer Bork*

EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany, 1MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK and 2Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK

SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models. This brings the total to over 600 domain families that are widely represented among nuclear, signalling and extracellular proteins. Annotation now includes links to the Online Mendelian Inheritance in Man (OMIM) database in cases where a human disease is associated with one or more mutations in a particular domain. We have implemented new analysis methods and updated others. New advanced queries provide direct access to the SMART relational database using SQL. This database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats. SMART output can now be easily included in users’ documents. A SMART mirror has been created at http://smart.ox.ac.uk.

* To whom correspondence should be addressed. Tel: +49 6221 387 526; Fax: +49 6221 387 519; Email: bork{at}embl-heidelberg.de Present address: Joerg Schultz, Cellzome, Meyerhofstrasse 1, 69012 Heidelberg, Germany


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E. Rescalli, S. Saini, C. Bartocci, L. Rychlewski, V. de Lorenzo, and G. Bertoni
Novel Physiological Modulation of the Pu Promoter of TOL Plasmid: NEGATIVE REGULATORY ROLE OF THE TURA PROTEIN OF PSEUDOMONAS PUTIDA IN THE RESPONSE TO SUBOPTIMAL GROWTH TEMPERATURES
J. Biol. Chem., February 27, 2004; 279(9): 7777 - 7784.
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 J. Appl. Physiol.Home page
M.-A. Gilles-Gonzalez and G. Gonzalez
Signal transduction by heme-containing PAS-domain proteins
J Appl Physiol, February 1, 2004; 96(2): 774 - 783.
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 Mol. Cell. Biol.Home page
D. Forler, G. Rabut, F. D. Ciccarelli, A. Herold, T. Kocher, R. Niggeweg, P. Bork, J. Ellenberg, and E. Izaurralde
RanBP2/Nup358 Provides a Major Binding Site for NXF1-p15 Dimers at the Nuclear Pore Complex and Functions in Nuclear mRNA Export
Mol. Cell. Biol., February 1, 2004; 24(3): 1155 - 1167.
[Abstract] [Full Text] [PDF]

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 Mol. Pharmacol.Home page
R. Zoraghi, J. D. Corbin, and S. H. Francis
Properties and Functions of GAF Domains in Cyclic Nucleotide Phosphodiesterases and Other Proteins
Mol. Pharmacol., February 1, 2004; 65(2): 267 - 278.
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 ScienceHome page
A. S. Yoo, C. Bais, and I. Greenwald
Crosstalk Between the EGFR and LIN-12/Notch Pathways in C. elegans Vulval Development
Science, January 30, 2004; 303(5658): 663 - 666.
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I. B. Zhulin
Digging with Experimental Pick and Computational Shovel: a New Addition to the Histidine Kinase Superfamily
J. Bacteriol., January 15, 2004; 186(2): 267 - 269.
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D. Broker, M. Arenskotter, A. Legatzki, D. H. Nies, and A. Steinbuchel
Characterization of the 101-Kilobase-Pair Megaplasmid pKB1, Isolated from the Rubber-Degrading Bacterium Gordonia westfalica Kb1
J. Bacteriol., January 1, 2004; 186(1): 212 - 225.
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 Mol. Endocrinol.Home page
O. Avsian-Kretchmer and A. J. W. Hsueh
Comparative Genomic Analysis of the Eight-Membered Ring Cystine Knot-Containing Bone Morphogenetic Protein Antagonists
Mol. Endocrinol., January 1, 2004; 18(1): 1 - 12.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
D. L. Wheeler, D. M. Church, R. Edgar, S. Federhen, W. Helmberg, T. L. Madden, J. U. Pontius, G. D. Schuler, L. M. Schriml, E. Sequeira, et al.
Database resources of the National Center for Biotechnology Information: update
Nucleic Acids Res., January 1, 2004; 32(90001): D35 - 40.
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 Nucleic Acids ResHome page
R. Apweiler, A. Bairoch, C. H. Wu, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, et al.
UniProt: the Universal Protein knowledgebase
Nucleic Acids Res., January 1, 2004; 32(90001): D115 - 119.
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 Nucleic Acids ResHome page
A. Bateman, L. Coin, R. Durbin, R. D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E. L. L. Sonnhammer, et al.
The Pfam protein families database
Nucleic Acids Res., January 1, 2004; 32(90001): D138 - 141.
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 Nucleic Acids ResHome page
I. Letunic, R. R. Copley, S. Schmidt, F. D. Ciccarelli, T. Doerks, J. Schultz, C. P. Ponting, and P. Bork
SMART 4.0: towards genomic data integration
Nucleic Acids Res., January 1, 2004; 32(90001): D142 - 144.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
A. Krupa, K. R. Abhinandan, and N. Srinivasan
KinG: a database of protein kinases in genomes
Nucleic Acids Res., January 1, 2004; 32(90001): D153 - 155.
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 Nucleic Acids ResHome page
K. Fleming, A. Muller, R. M. MacCallum, and M. J. E. Sternberg
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
Nucleic Acids Res., January 1, 2004; 32(90001): D245 - 250.
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M. Chen, S. Lin, and R. Hofestaedt
STCDB: Signal Transduction Classification Database
Nucleic Acids Res., January 1, 2004; 32(90001): D456 - 458.
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B. Huang, C. B. Whitchurch, and J. S. Mattick
FimX, a Multidomain Protein Connecting Environmental Signals to Twitching Motility in Pseudomonas aeruginosa
J. Bacteriol., December 15, 2003; 185(24): 7068 - 7076.
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C.-T. Thai and R. T. Ogata
Expression and Characterization of the C345C/NTR Domains of Complement Components C3 and C5
J. Immunol., December 15, 2003; 171(12): 6565 - 6573.
[Abstract] [Full Text] [PDF]

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 Eukaryot CellHome page
E. Villalobo, C. Moch, G. Fryd-Versavel, A. Fleury-Aubusson, and L. Morin
Cysteine Proteases and Cell Differentiation: Excystment of the Ciliated Protist Sterkiella histriomuscorum
Eukaryot. Cell, December 1, 2003; 2(6): 1234 - 1245.
[Abstract] [Full Text] [PDF]

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 Protein Eng Des SelHome page
A. Bhaduri and R. Sowdhamini
A genome-wide survey of human tyrosine phosphatases
Protein Eng. Des. Sel., December 1, 2003; 16(12): 881 - 888.
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Y. Noda, M. Kohjima, T. Izaki, K. Ota, S. Yoshinaga, F. Inagaki, T. Ito, and H. Sumimoto
Molecular Recognition in Dimerization between PB1 Domains
J. Biol. Chem., October 31, 2003; 278(44): 43516 - 43524.
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H. Tateno and I. J. Goldstein
Molecular Cloning, Expression, and Characterization of Novel Hemolytic Lectins from the Mushroom Laetiporus sulphureus, Which Show Homology to Bacterial Toxins
J. Biol. Chem., October 17, 2003; 278(42): 40455 - 40463.
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 Genes Dev.Home page
N. Kamei and C. G. Glabe
The species-specific egg receptor for sea urchin sperm adhesion is EBR1,a novel ADAMTS protein
Genes & Dev., October 15, 2003; 17(20): 2502 - 2507.
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C. A. Innis and M. Hyvonen
Crystal Structures of the Heparan Sulfate-binding Domain of Follistatin: INSIGHTS INTO LIGAND BINDING
J. Biol. Chem., October 10, 2003; 278(41): 39969 - 39977.
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B. Ciani, R. Layfield, J. R. Cavey, P. W. Sheppard, and M. S. Searle
Structure of the Ubiquitin-associated Domain of p62 (SQSTM1) and Implications for Mutations That Cause Paget's Disease of Bone
J. Biol. Chem., September 26, 2003; 278(39): 37409 - 37412.
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 Genome ResHome page
P. D. Thomas, M. J. Campbell, A. Kejariwal, H. Mi, B. Karlak, R. Daverman, K. Diemer, A. Muruganujan, and A. Narechania
PANTHER: A Library of Protein Families and Subfamilies Indexed by Function
Genome Res., September 1, 2003; 13(9): 2129 - 2141.
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 Mol. Biol. CellHome page
K. Hirota, K. Tanaka, K. Ohta, and M. Yamamoto
Gef1p and Scd1p, the Two GDP-GTP Exchange Factors for Cdc42p, Form a Ring Structure that Shrinks during Cytokinesis in Schizosaccharomyces pombe
Mol. Biol. Cell, September 1, 2003; 14(9): 3617 - 3627.
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 ScienceHome page
N. King, C. T. Hittinger, and S. B. Carroll
Evolution of Key Cell Signaling and Adhesion Protein Families Predates Animal Origins
Science, July 18, 2003; 301(5631): 361 - 363.
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 Nucleic Acids ResHome page
M. M. S. Bharath, N. R. Chandra, and M. R. S. Rao
Molecular modeling of the chromatosome particle
Nucleic Acids Res., July 15, 2003; 31(14): 4264 - 4274.
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K. Asamitsu, T. Tetsuka, S. Kanazawa, and T. Okamoto
RING Finger Protein AO7 Supports NF-{kappa}B-mediated Transcription by Interacting with the Transactivation Domain of the p65 Subunit
J. Biol. Chem., July 11, 2003; 278(29): 26879 - 26887.
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 Nucleic Acids ResHome page
P. Puntervoll, R. Linding, C. Gemund, S. Chabanis-Davidson, M. Mattingsdal, S. Cameron, D. M. A. Martin, G. Ausiello, B. Brannetti, A. Costantini, et al.
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
Nucleic Acids Res., July 1, 2003; 31(13): 3625 - 3630.
[Abstract] [Full Text] [PDF]


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