Difference between revisions of "PrePPI"
From LMU BioDB 2013
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#The database is maintained by the [http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page Honig Lab] of Columbia University and the Howard Hughes Medical Institute (refer to http://bhapp.c2b2.columbia.edu/PrePPI/about.html). | #The database is maintained by the [http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page Honig Lab] of Columbia University and the Howard Hughes Medical Institute (refer to http://bhapp.c2b2.columbia.edu/PrePPI/about.html). | ||
#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). | #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). | ||
| + | #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. | ||
==Presentation== | ==Presentation== | ||
[[User:Ksherbina|'''Katrina Sherbina''']] and [[User:Gleis|'''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. | [[User:Ksherbina|'''Katrina Sherbina''']] and [[User:Gleis|'''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. | ||
Revision as of 01:07, 30 September 2013
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
- The database accessed was PrePP, a database for protein-protein interactions. Visit the site at: http://bhapp.c2b2.columbia.edu/PrePPI/
- 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/
- 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/
- 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/
- It can answer questions of protein interactions, probability of interaction, and structure of interacting proteins.
- 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
- 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).
- 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).
- 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.
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.
