Proteomics/Protein - Protein Interactions/Databases
Page Edited and Updated by: Dan Surdyk
E-mail: dfs6389@rit.edu
This Section:
Databases
editThere are many databases available containing protein interaction data. The data can be derived from experimental results, computational predictions, automated literature mining, or manual curation of the literature. Some sites allow you to view networks of interactions graphically. The following list contains a variety of databases, all of which are free for academic use. They were last accessed 19 April 2006, but with the rapidly changing world of proteomics/bioinformatics, we make no guarantees that they are still functional.
Species Specific
editSaccharomyces cerevisiae (yeast)
edit- Yeast GRID
- Part of The GRID (General Repository for Interaction Datasets)
- The Tyers Group at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital
- http://www.thebiogrid.org
- Can be viewed with Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index)
Homo sapiens (human)
edit- Biomolecular Interaction Network Database (BIND)
- Unleashed Informatics
- http://www.bind.ca/Action
- Contains curated interaction data for human proteins. Requires users to register for free Unleashed Informatics account.
- Human Protein Interaction Database
- Web Intelligence Lab, Department of computer Science and Information Engineering, Inha University
- http://wilab.inha.ac.kr/hpid/
- Integrates several known databases and makes some novel predictions.
Drosophila melanogaster (fruit fly)
edit- Drosophila Interactions Database
- Finley lab, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine
- http://proteome.wayne.edu/PIMdb.html
- Use IM Browser (see information on page) to query the database and get the results as interactive graphs.
- Fly GRID
- Part of The GRID (General Repository for Interaction Datasets)
- The Tyers Group at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital
- http://www.thebiogrid.org
- Can be viewed with Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index)
Helicobacter pylori
edit- Helicobacter Pylori Database of Protein Interactomes
- http://dpi.nhri.org.tw/protein/hp/ORF/index.php
- Select a protein and provide an interaction cutoff to see a graphical interaction map.
Caenorhabditis elegans
edit- Worm GRID
- Part of The GRID (General Repository for Interaction Datasets)
- The Tyers Group at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital
- http://www.thebiogrid.org
- Can be viewed with Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index)
Multiple Species
edit- PIMRider
- Hybrigenics
- http://pim.hybrigenics.com/pimriderext/common/
- Several databases are available for viewing with PIMRider: drosophila, H. pylori, HIV, and human TGF-beta signalling related proteins. Requires free registration.
- HIV-1, human protein interaction database
- National Institute of Allergy and Infectious Diseases, NCBI
- http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/
- Contains interactions between HIV and host proteins, as obtained from literature.
- Database of interacting proteins
- UCLA
- http://dip.doe-mbi.ucla.edu/
- Interaction data from literature and other databases.
- A Molecular Interactions Database (MINT)
- The “MINTers”: http://mint.bio.uniroma2.it/mint/contacts.do
- http://mint.bio.uniroma2.it/mint/
- Focuses on experimentally verified protein interactions, especially those in mammals.
- Munich Information Center for Protein Sequences (MIPS)
- A manually curated database of protein-protein interactions in mammals.
- Also contains info about other protein-protein interaction projects.
- http://mips.gsf.de/proj/ppi/
- Jena Center for Bioinformatics
- Excellent Protein-Protein interaction website for general information
- http://www.imb-jena.de/jcb/ppi/