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NAR Molecular Biology Database Collection entry number 787
W. Zhang1, Y. Zhang1, H. Zheng2, C. Zhang3, W. Xiong 2,J.G. Olyarchuk 1, M. Walker 4, W. Xu 5, M. Zhao 1, S. Zhao 1 , Z. Zhou 2 and L. Wei1
1Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P.R. China
2 Institute of Molecular Medicine, Peking University, Beijing 100871, P.R. China
3 Center for Basic Neuroscience, UT Southwestern Medical Center, Dallas, TX 75235, USA
4 Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA5 Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA

Database Description

Synaptic protein database (SynDB, available at, is a manually curated database of the molecular biology of the synapse proteome. It contains a comprehensive collection of proteins (13580 unique proteins spanning 650 species and 264 domain families) known or predicted to be associated with synaptic activities and functions, and extensive information on protein functions, sequences, structures, expression, pathways, interactions, and disease associations. SynDB might serve as a repository for current knowledge as well as a starting point for future neurobiological and neuroinformatic research.

To describe synaptic structures and functions we have developed Synapse Ontology (SynO). SynDB can be interactively browsed by Synapse Ontology, Gene Ontology, domain families, species, chromosomal locations, or Tribe-MCL clusters. It can also be searched by text (including Boolean operators) or by sequence similarity. To our knowledge, SynDB is the first focused yet comprehensive database for synaptic proteins.


We are grateful to all the collaboraters, who reviewed our database and gave us kind advice.


1. Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M. et al. (2004) UniProt: the Universal Protein knowledgebase. Nucl. Acids Res., 32, D115-119.
2. Cowan, W.M, Sudhof, T.C, Stevens, C.F., and Davies, K. (2000) Synapses. The Johns Hopkins University Press, Baltimore and London.
3. Kandel, E.R., Schwartz, J.H., and Jessell, T.M. (2000) Principles of Neural Science. 4 ed. McGraw-Hill Companies.
4. Hille, B. (2001) Ion Channels of Excitable Membranes. 3 ed. Sinauer Associates,Inc.

Go to the abstract in the NAR 2007 Database Issue.
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