Education
1978 Ph.D., Northwestern University
1974 B.A., Reed College

Honors and Awards
1987 Alfred P. Sloan Foundation Fellowship
1989 Excellence in Teaching Award
1997 Sequoyah Fellow, American Indian Science and Engineering Society

Research Interests
The group of Prof. Ondrechen works in the areas of theoretical and computational chemistry and chemical biology. Areas of interest include functional genomics - prediction of the functional roles of gene products (proteins), modeling of enzyme-substrate interactions, bioinformatics, rational design of materials, non-linear optical properties of polymers, and modeling for proteomics applications. With the sequencing of the human genome and the genomes of hundreds of other species, structural genomics efforts are enabling the discovery of thousands of new protein structures. The next question is: What do these structures actually do? Prof. Ondrechen’s group is working on the development of methods to predict protein function from structure. Our THEMATICS method (see Ondrechen et al., Proc. Natl. Acad. Sci. USA 98, 12473, 2001) requires only the structure of the subject protein and thus works for proteins that bear no resemblance to previously characterized proteins.

Current projects deal with: 1) Using THEMATICS for the analysis of specific enzymes of biological and medical importance; 2) Investigating combined methods in order to predict functional information from only the sequence; 3) Comparison of THEMATICS analyses with the evolutionary history; and 4) Development and application of an automated version of THEMATICS to computationally screen large numbers of protein structures. We are working in partnership with the Institute for Complex Scientific Software (ICSS) at Northeastern University on the automated version of THEMATICS. We are also building Quantum Mechanical / Molecular Mechanical (QM/MM) models for enzyme-substrate interactions, in order to understand better how enzymes affect catalysis. Current (QM/MM) projects deal with enzymes that use vitamin B6 as a cofactor.

(The picture shows the vitamin B6 Schiff base inside the active site of the enzyme Alanine racemase).

Selected Publications

Wei, Ying; Ko, Jaeju; Murga, Leonel F.; Ondrechen, Mary Jo. Selective prediction of interaction sites in protein structures with THEMATICS. BMC Bioinformatics (2007), 8.

Wei, Ying; Ringe, Dagmar; Wilson, Mark A.; Ondrechen, Mary Jo. Identification of functional subclasses in the DJ-1 superfamily proteins. PLoS Computational Biology (2007), 3(1), 120-126.

Shehadi, Ihsan A.; Abyzov, Alexej; Uzun, Alper; Wei, Ying; Murga, Leonel F.; Ilyin, Valentin; Ondrechen, Mary Jo. Active site prediction for comparative model structures with THEMATICS. Journal of Bioinformatics and Computational Biology (2005), 3(1), 127-143