Structural Bioinformatics

Overview:

The goal of the project is to develop algorithms for predicting the molecular function of a protein from a structural model of its active sites. Given the 3D atomic coordinates for a novel protein and the location of a ligand binding site, we build a model of the site cavity, match it against a database of active sites models having known molecular functions, and make predictions based on the functional annotations associated with the best matches.

Abstracts and Publications:

Thomas A. Funkhouser, Roman A. Laskowski, and Janet M. Thornton,
Finding and Extracting Active Site Cavities in Proteins,
Structural Bioinformatics and Computational Biophysics Meeting (3DSIG), Vienna, Austria, July 2007.
Thomas A. Funkhouser, Roman A. Laskowski, and Janet M. Thornton,
Protein Function Prediction by Matching Volumetric Models of Active Sites,
Automated Function Prediction Meeting (AFP), San Diego, CA, August 2006.
Thomas A. Funkhouser, Roman A. Laskowski, and Janet M. Thornton,
Matching Volumetric Models of Protein Active Sites,
Structural Bioinformatics and Computational Biophysics Meeting (3DSIG), Fortaleza, Brazil, July 2006.

Courses:

COS 597A (Fall 2005) -- Structural Bioinformatics
COS 597A (Fall 2007) -- Structural Bioinformatics

Resources:

Bibliography

Acknowledgements:

National Science Foundation (IIS-0612231)