PPT-DB -- the Protein property Prediction and Testing DataBase
URL:
What you can do:
Locate commonly predicted protein property information.
Highlights:
- Properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. order parameters, B-factors, folding rates) features that have been measured, derived or tabulated from a variety of sources.
- PPT-DB is designed to serve as a centralized, up-to-date, freely downloadable and easily queried repository of predictable or 'derived' protein property data. In this role, PPT-DB can serve as a one-stop, fully standardized repository for developers to obtain the required training, testing and validation data needed for almost any kind of protein property prediction program they may wish to create.
- The second role that PPT-DB can play is as a tool for homology-based protein property prediction. Users may query PPT-DB with a sequence of interest and have a specific property predicted using a sequence similarity search against PPT-DB's extensive collection of proteins with known properties.
- PPT-DB exploits the well-known fact that protein structure and dynamic properties are highly conserved between homologous proteins.
- Predictions derived from PPT-DB's similarity searches are typically 85-95% correct (for categorical predictions, such as secondary structure) or exhibit correlations of >0.80 (for numeric predictions, such as accessible surface area). This performance is 10-20% better than what is typically obtained from standard 'ab initio' predictions.
Keywords:
- Protein Conformation
- Amino Acid Sequence Homology
- protein property prediction
- protein properties
- protein structure
- protein property data
Literature & Tutorials:
This record last updated: 05-02-2008