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Nucleic Acids Research, 2004, Vol. 32, Database issue D115-D119
© 2004 Oxford University Press

UniProt: the Universal Protein knowledgebase

Rolf Apweiler*, Amos Bairoch1, Cathy H. Wu2, Winona C. Barker3, Brigitte Boeckmann1, Serenella Ferro1, Elisabeth Gasteiger1, Hongzhan Huang2, Rodrigo Lopez, Michele Magrane, Maria J. Martin, Darren A. Natale2, Claire O’Donovan, Nicole Redaschi1 and Lai-Su L. Yeh3

The EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 1 Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland, 2 Department of Biochemistry and Molecular Biology and 3 National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057-1414, USA

*To whom correspondence should be addressed. Tel: +44 1223 494435; Fax: +44 1223 494468; Email: apweiler{at}ebi.ac.uk

To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.


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R. Petryszak, E. Kretschmann, D. Wieser, and R. Apweiler
The predictive power of the CluSTr database
Bioinformatics, September 15, 2005; 21(18): 3604 - 3609.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
J. Espadaler, O. Romero-Isart, R. M. Jackson, and B. Oliva
Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships
Bioinformatics, August 15, 2005; 21(16): 3360 - 3368.
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 Nucleic Acids ResHome page
J. E. Donald and E. I. Shakhnovich
Predicting specificity-determining residues in two large eukaryotic transcription factor families
Nucleic Acids Res., August 5, 2005; 33(14): 4455 - 4465.
[Abstract] [Full Text] [PDF]

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 MicrobiologyHome page
C. Baker-Austin, M. Dopson, M. Wexler, R. G. Sawers, and P. L. Bond
Molecular insight into extreme copper resistance in the extremophilic archaeon 'Ferroplasma acidarmanus' Fer1
Microbiology, August 1, 2005; 151(8): 2637 - 2646.
[Abstract] [Full Text] [PDF]

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 J. Bacteriol.Home page
J. Boekhorst, M. W. H. J. de Been, M. Kleerebezem, and R. J. Siezen
Genome-Wide Detection and Analysis of Cell Wall-Bound Proteins with LPxTG-Like Sorting Motifs
J. Bacteriol., July 15, 2005; 187(14): 4928 - 4934.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
P. Jones, N. Vinod, T. Down, A. Hackmann, A. Kahari, E. Kretschmann, A. Quinn, D. Wieser, H. Hermjakob, and R. Apweiler
Dasty and UniProt DAS: a perfect pair for protein feature visualization
Bioinformatics, July 15, 2005; 21(14): 3198 - 3199.
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 ScienceHome page
A. Pain, H. Renauld, M. Berriman, L. Murphy, C. A. Yeats, W. Weir, A. Kerhornou, M. Aslett, R. Bishop, C. Bouchier, et al.
Genome of the Host-Cell Transforming Parasite Theileria annulata Compared with T. parva
Science, July 1, 2005; 309(5731): 131 - 133.
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 Nucleic Acids ResHome page
S. Pillai, V. Silventoinen, K. Kallio, M. Senger, S. Sobhany, J. Tate, S. Velankar, A. Golovin, K. Henrick, P. Rice, et al.
SOAP-based services provided by the European Bioinformatics Institute
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W25 - W28.
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 Nucleic Acids ResHome page
R. A. Laskowski, J. D. Watson, and J. M. Thornton
ProFunc: a server for predicting protein function from 3D structure
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W89 - W93.
[Abstract] [Full Text] [PDF]


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