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Mary Jo Ondrechen

122 Hurtig Hall
360 Huntington Avenue
Boston, MA 02115


Prof. Ondrechen’s research group specializes in theoretical and computational chemistry and computational biology. Areas of interest include: 1) Understanding the fundamental basis for enzyme catalysis; 2) Functional genomics – prediction of the functional roles of gene products (proteins); 3) Modeling of enzyme-substrate interactions; 4) Drug discovery; and 5) Bioinformatics.

With the sequencing of the human genome and the genomes of hundreds of species of interest, Structural Genomics (SG) projects have now reported over 12,000 new protein structures. The next question is: What do these structures actually do? Prof. Ondrechen’s group is developing methods to predict protein function from structure. Our THEMATICS (see Ondrechen et al., Proc. Natl. Acad. Sci. USA 98, 12473, 2001) and POOL (see Tong, Wei, Murga, Ondrechen and Williams, PLoS Computational Biology, 2009) methods predict the residues involved in biochemical function, require only the structure of the query protein, and thus work for proteins that bear no resemblance to previously characterized proteins. Our SALSA method (see Wang, Yin, et al. 2013) uses these predicted functional residues to determine biochemical function.

Another current project explores the multilayer nature of enzyme active sites – we are able to predict when remote amino acid residues are involved in catalysis. We work in collaboration with experimentalists to test and verify our predictions pertaining to multilayer active sites.


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

Research & Scholarship Interests

Theoretical chemical biology/physics
Affiliated With

Department Research Areas

College Research Initiatives

Selected Publications

  • E. Mongeau, G. Yuan, Z. Minden, S. Waldron, R. Booth, D. Felsing, M.J. Ondrechen, G.B. Jones, Homology Modeling Inspired Synthesis of 5-HT2A Inhibitors: A Diazepine Analogue of the Atypical Antipsychotic JL13, Central Nervous System Agents in Medicinal Chemistry, 2017
  • R. Parasuram, C.L. Mills, Z. Wang, S. Somasundaram, P.J. Beuning, M.J. Ondrechen, Local Structure Based Method for Prediction of the Biochemical Function of Proteins: Application to Glycoside Hydrolases, Methods, 93, 2016, 51-63
  • C.L. Mills, P.J. Beuning, M.J. Ondrechen, Biochemical Functional Predictions for Protein Structures of Unknown or Uncertain Function, Computational and Structural Biotechnology Journal, 13, 2015, 182-191
  • H.R. Brodkin, N.A. DeLateur, S. Somarowthu, C.L. Mills, W.R. Novak, P.J. Beuning, D. Ringe, M.J. Ondrechen, Prediction of Distal Residue Participation in Enzyme Catalysis, Protein Science, 24(5), 2015, 762-778
  • R.N. Hanson, P. Tongcharoensirikul, K. Barnsley, M.J. Ondrechen, A. Hughes, E.R. DeSombre, Synthesis and Evaluation of 2-halogenated-1,1-bis(4-hydroxyphenyl)-2-(3-hydroxyphenyl)-ethylenes as Potential Estrogen Receptor-targeted Radiodiagnostic and Radiotherapeutic Agents, Steroids, 96, 2015, 50-62