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

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.