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Nucleic Acids Research, 2002, Vol. 30, No. 1 303-305
© 2002 Oxford University Press

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

Ioannis Xenarios, Lukasz Salwínski, Xiaoqun Joyce Duan, Patrick Higney, Sul-Min Kim and David Eisenberg*

UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, PO Box 951570, UCLA, Los Angeles, CA 90095-1570, USA

The Database of Interacting Proteins (DIP: http://dip.doe-mbi.ucla.edu) is a database that documents experimentally determined protein–protein interactions. It provides the scientific community with an integrated set of tools for browsing and extracting information about protein interaction networks. As of September 2001, the DIP catalogs ~11 000 unique interactions among 5900 proteins from >80 organisms; the vast majority from yeast, Helicobacter pylori and human. Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein–protein interactions available in the DIP database.

* To whom correspondence should be addressed. Tel: +1 310 825 3754; Fax: +1 310 206 3914; Email: david{at}mbi.ucla.edu The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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E. Kolker, K. S. Makarova, S. Shabalina, A. F. Picone, S. Purvine, T. Holzman, T. Cherny, D. Armbruster, R. S. Munson Jr, G. Kolesov, et al.
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
Nucleic Acids Res., April 30, 2004; 32(8): 2353 - 2361.
[Abstract] [Full Text] [PDF]


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Proc. Natl. Acad. Sci. USAHome page
A. Fernandez, R. Scott, and R. S. Berry
The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks
PNAS, March 2, 2004; 101(9): 2823 - 2827.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
H. Yu, X. Zhu, D. Greenbaum, J. Karro, and M. Gerstein
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics
Nucleic Acids Res., January 14, 2004; 32(1): 328 - 337.
[Abstract] [Full Text] [PDF]


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Mol. Cell. ProteomicsHome page
A.-C. Tien, M.-H. Lin, L.-J. Su, Y.-R. Hong, T.-S. Cheng, Y.-C. G. Lee, W.-J. Lin, I. H. Still, and C.-Y. F. Huang
Identification of the Substrates and Interaction Proteins of Aurora Kinases from a Protein-Protein Interaction Model
Mol. Cell. Proteomics, January 1, 2004; 3(1): 93 - 104.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
C. Lemer, E. Antezana, F. Couche, F. Fays, X. Santolaria, R.'s Janky, Y. Deville, J. Richelle, and S. J. Wodak
The aMAZE LightBench: a web interface to a relational database of cellular processes
Nucleic Acids Res., January 1, 2004; 32(90001): D443 - 448.
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Nucleic Acids ResHome page
L. Salwinski, C. S. Miller, A. J. Smith, F. K. Pettit, J. U. Bowie, and D. Eisenberg
The Database of Interacting Proteins: 2004 update
Nucleic Acids Res., January 1, 2004; 32(90001): D449 - 451.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
H. Hermjakob, L. Montecchi-Palazzi, C. Lewington, S. Mudali, S. Kerrien, S. Orchard, M. Vingron, B. Roechert, P. Roepstorff, A. Valencia, et al.
IntAct: an open source molecular interaction database
Nucleic Acids Res., January 1, 2004; 32(90001): D452 - 455.
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Nucleic Acids ResHome page
D. Cotter, P. Guda, E. Fahy, and S. Subramaniam
MitoProteome: mitochondrial protein sequence database and annotation system
Nucleic Acids Res., January 1, 2004; 32(90001): D463 - 467.
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Sci SignalHome page
I. Stagljar
Finding Partners: Emerging Protein Interaction Technologies Applied to Signaling Networks
Sci. Signal., December 16, 2003; 2003(213): pe56 - pe56.
[Abstract] [Full Text] [PDF]



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