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Bioinformatics Advance Access published online on March 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti366
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 1, 2004
Revised January 27, 2005
Accepted February 28, 2005

Applications note

PSIbase: a database of Protein Structural Interactome map (PSIMAP)

Sungsam Gong 1, Giseok Yoon 2, Insoo Jang 3, Dan Bolser 4, Panos Dafas 5, Michael Schroeder 6, Hansol Choi 1, Yoobok Cho 2, Kyungsook Han 7, Sunghoon Lee 3, Hwanho Choi 1, Michael Lappe 8, Liisa Holm 9, Sangsoo Kim 3, Donghoon Oh 2, and Jonghwa Bhak 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 Max Planck Institute for Molecular Genetics, Berlin, Germany
9 Helsinki University, Finland
10 Biomatics Lab, Dept. of BioSystems, KAIST, Daejeon, Korea; OITEK, Daejeon, Korea; NGIC, KRIBB, Daejeon, Korea; BiO centre, KAIST, Daejeon, Korea

* To whom correspondence should be addressed.
Jonghwa Bhak, E-mail: biopark{at}kaist.ac.kr


  Abstract

Summary: Protein Structural Interactome map (PSIMAP) is a global interaction map that describes domain-domain and protein-protein interaction information for known PDB (Protein Data Bank) structures. It calculates Euclidean distance to determine interactions between possible pairs of structural domains in proteins. PSIbase is a database and file server for protein structural interaction information calculated by the PSIMAP algorithm. PSIbase also provides an easy-to-use protein domain assignment module, interaction navigation, and visual tools. Users can retrieve possible interaction partners of their proteins of interests if a significant homology assignment is made with their query sequences.

Availability: http://psimap.org and http://psibase.kaist.ac.kr/.

Supplementary information: Supplementary material is available at http://psibase.kaist.ac.kr/Download/supplementary_material_for_download.doc.


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