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Bioinformatics Advance Access originally published online on March 3, 2005
Bioinformatics 2005 21(10):2541-2543; 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{at}oupjournals.org

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 1,2,3,10,*

1Biomatics Lab, Department of BioSystems, KAIST Daejeon, Korea
2OITEK Daejeon, Korea
3NGIC, KRIBB Daejeon, Korea
4MRC-DUNN Cambridge, UK
5City University London, UK
6Biotechnologisches Zentrum TU Dresden, Germany
7Inha University Incheon, Korea
8Max Planck Institute for Molecular Genetics Berlin, Germany
9Helsinki University Finland
10BiO Centre, KAIST Daejeon, Korea

*To whom correspondence should be addressed.

Summary: Protein Structural Interactome map (PSIMAP) is a global interaction map that describes domain–domain and protein–protein interaction information for known Protein Data Bank structures. It calculates the 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/

Contact: biopark{at}kaist.ac.kr

Supplementary information: Supplementary material is available at http://psibase.kaist.ac.kr/Doc/supplementary_material.htm


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