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 PrePPI, 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 amino acid sequence information for interacting proteins, functional information about protein of interest, and links to experimental evidence of protein-protein interactions. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531098/
4. The site includes information for Saccharomyces cerevisiae and human proteins. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531098/
5. It can answer questions of protein interactions, probability of interaction, and possible structure of interacting proteins.
6. This is an electronically 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).
13. The site is well-organized. The home page is simple with the search box easy to find and all acceptable queries defined below the search box. In looking up a query, the search results were presented in a clear, tabular format. The predicted interactions were listed in order of decreasing likelihood of interaction. The home page and results pages contain a navigation tool bar with links to the "help" page and "about" page. The help page contains basic information about using the database and the derivation of the information on the database however, there is no step-by-step tutorial explaining how to use the database.

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. The PowerPoint presentation can be viewed here.