Proteomics/Protein - Protein Interactions/Databases

Page Edited and Updated by: Dan Surdyk
E-mail: dfs6389@rit.edu

This Section:

Databases

There 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

Saccharomyces cerevisiae (yeast)

• 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)

• 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)

• 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

• 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

• 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

• 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/