ARLO RANDALL


Home Department
Information and Computer Science

Thesis Advisor
Pierre Baldi – Information and Computer Science

Co-thesis Advisor
Luis Villarreal - Molecular Biology and Biochemistry

Email


Arlo Randall is developing a database of structural information on proteins from viruses in the poxvirus family. For 3D structure the database is populated with solved structures, homology predictions, and ab initio predictions. Other types of structural information in the database include secondary structure (predicted or determined by DSSP) and relative solvent accessibility of residues. The database also includes general information about each protein and lists of homologues using multiple sets of criteria. Arlo is also developing a web interface which provides easy access to the information. [Poxvirus Structural Proteomics Database (PSPDB). Access: www.igb.uci.edu/tools.htm.]

Arlo is also building a database of short peptides sequences and their structures, using the Protein Data Bank as his source of structural information. The short peptide structures (k-mers) can then be utilized in protein reconstruction, because sequential homology often implies structural homology-even on this very small scale. The k-mer libraries will be utilized by Pierre Baldi’s lab as one component of a larger effort in protein structure prediction. This project is related to the above project because the 3D protein predictions will be incorporated into the database described above.

Publications

A.Z. Randall, P.F. Baldi and L.P. Villarreal. Structural Proteomics of the Pox virus Family. Artificial Intelligence in Medicine. Journal, special issue on “Data Mining in Genomics and Proteomics”, in press (2003).