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PSIbase


NAR Molecular Biology Database Collection entry number 616
Gong, S.1, Yoon, G. 2, Jang, I. 3, Bolser, D. 4, Dafas, P. 5, Schroeder, M. 6, Choi, S. 1, Lee, S. 1, Cho, Y. 2, Han, K. 7, Lee, S. 3, Lappe, M. 8, Holm, L. 9, Kim, S. 3, Oh, D. 2, Bhak, J. 1,2,3,10
1 Biomatics Lab, Dept. of BioSystems, KAIST, Daejeon, Korea
2 OITEK, Daejeon, Korea
3 NGIC, KRIBB, Daejeon, Korea
4 MRC-DUNN, Cambridge, UK
5 City University, London, UK
6 Biotechnologisches Zentrum, TU Dresden, Germany
7 Inha University, Incheon, Korea
8 Cambridge University, Cambridge, UK
9 Helsinki University, Finland
10 BiO centre, KAIST, DaeJeon, Korea

Database Description

Protein Structural Interactome MAP or PSIMAP is a protocol and a global protein and domain interaction map that calculates domain-domain and protein-protein interaction information from proteins whose structures are known. PSIbase (http://psimap.kaist.ac.kr) is the database server of PSIMAP (http://psimap.org). The PSIbase serves protein structural interaction data. There are three types of interaction data sources at present: FAC, SAC and BBC PSIMAP. PSIbase also provides FASTA format interacting protein sequences and shows interacting interfaces of proteins from PDB by visualization tool called InterFacer. For easier access for biological users, PSIbase contains a domain assignment component where interaction partners can be predicted after homology assignment of query sequence using an intermediate sequence library or ISL. As of May 2004, PSIbase contains 1895 unique protein domain nodes and 2655 unique edges at SCOP Family level (Superfamily level interaction is derived from the family interaction level automatically).

Acknowledgements

We thank Mr. Chung MoonSoul for donating $25 million USD for the department of Biosystems at KAIST. This project was funded partly by IMT-2000 C3-4 grants of ministry of information and communication department of Korea. JHB is partly supported by Biogreen21. PSIbase is developed and maintained by OITEK Inc in collaboration with the BiO centre, Biomatics Lab of KAIST and Biomatics lab of NGIC, KRIBB of Korea.

References

1. Kim WK, Bolser DM, Park JH. Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics. 2004, 20: 1138-1150.
2. Park J, Lappe M, Teichmann SA. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol. 2001, 307: 929-938.
3. Lappe M, Park J, Niggemann O, Holm L. Generating protein interaction maps from incomplete data: application to fold assignment. Bioinformatics. 2001, 17: S149-S156
4. Gong S, Yoon G, Jang I. PSIbase: a database of Protein Structural Interactome map (PSIMAP) Bioinformatics 2005.
5. Park D, Lee S, Bolser D. Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Bioinformatics 2005


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