PrePPI

Information was gathered on the PrePPI database as part of the Week 5 Assignment for the Biological Databases class. For information regarding other databases explored by other students for this assignment, go to the page Class Journal Week 5.

Information Regarding the Database

1. The database accessed was PrePP, a database for protein-protein interactions. Visit the site at: http://bhapp.c2b2.columbia.edu/PrePPI/
2. The purpose of the database is to catalogue a combination of predicted and experimentally determined protein interactions. Additionally the database assigns probabilities to protein-protein interactions using an extensive multi-variable algorithm. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531098/
3. Biological information on the site includes genome wide protein protein interaction studies, structural models of PPIs, protein function information, and nomenclature information. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531098/
4. The site includes information for Saccharomyces cerevisiae, human, arabidopsis, Drosophila melanogaster, C. elegans, and E. Coli among others. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531098/
5. It can answer questions of protein interactions, probability of interaction, and structure of interacting proteins.
6. This is a "in-house" curated "meta" site representing structure, model organism, and molecular interactions. http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page
7. The database is maintained by the Honig Lab of Columbia University and the Howard Hughes Medical Institute (refer to http://bhapp.c2b2.columbia.edu/PrePPI/about.html).
8. This project is funded by multiple grants from the National Institutes of Health as well as a China Scholarship Council scholarship (refer to the "Acknowledgments" section in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3482288/#SD1).
9. Commercial and academic institutions need to contact the Honig lab to obtain a license to download the database for research use (refer to #9 in the FAQ in http://bhapp.c2b2.columbia.edu/PrePPI/help.html.
10. The current version of the database was released on 1/27/2012 (refer to http://bhapp.c2b2.columbia.edu/PrePPI/about.html).
11. When looking up a protein of interest, the results page will provide a link to the entry for the protein in the UniProt database (for example, click on the ID next to "Query protein" in http://bhapp.c2b2.columbia.edu/PrePPI/cgi-bin/search.cgi?query=P03989&protein=P03989). The database also links to the Protein Data Bank for those protein-protein interactions for which a structural model with high confidence was determined (click on the link designated by an arrow in a box in the "Template" row in http://bhapp.c2b2.columbia.edu/PrePPI/html/tmp/P03989_Q95460/model.htm).
12. Information regarding all the protein-protein interactions determined for a query protein can be downloaded as a text file (refer to the "The PrePPI Database: Web Interface" section in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531098/#__sec6title).

Presentation

Katrina Sherbina and Gabriel Leis will present information regarding the structure of the database and how to use it on Thursday, October 3, 2013 during the Biological Databases class.