Welcome to the PPT-DB! PPT-DB is a database of protein property databases. PPT-DB can be used by both software developers and protein chemists. To use the database, click on any of the database links on the left margin. Users can download the databases, search by text or search by sequence. Learn more about the database by clicking the navigation buttons located at the top of this page.
Protein Chemists can use PPT-DB to accurately predict (via sequence homology):
1) Secondary structure (helices, beta strands, beta turns, transmembrane helices, etc.)
2) 3D structure parameters (disulfide bonding pairs, contact order, salt bridges)
3) Protein dynamics (order parameters, RMSF, B-factors)
4) Protein signaling motifs (gram +/gram - and eukaryotic signal peptides)
5) Protein folding rates (ln(k), contact order, secondary structure content)
Software Developers can use PPT-DB as a one-stop-shop to obtain high quality data sets to train, test, evaluate and validate protein property prediction software including:
1) Secondary structure prediction software
2) Protein flexibility/epitope prediction software
3) Transmembrane helix, signal peptide and beta barrel prediction software
4) 3D structure prediction software
5) Miscellaneous properties (protein folding rates, disulfide bond pairs, contact order)
Users and developers are invited to suggest or submit additions, enhancements or corrections to the database.
Please cite: David S. Wishart, David Arndt, Mark Berjanskii, An Chi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou and Guohui Lin: PPT-DB: the protein property prediction and testing database. Nucleic Acids Research 2008 36(Database issue):D222-D229.
This project is supported by Genome Alberta & Genome Canada, a not-for-profit organization that is leading Canada's national genomics strategy with $600 million in funding from the federal government.