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Mary Jo Ondrechen

Mary Jo Ondrechen


Mailing Address:

335 ISEC (Interdisciplinary Science and Engineering Complex), Boston, MA 02115

Office Address:

312 ISEC (Interdisciplinary Science and Engineering Complex), Boston, MA 02115


  • bioinformatics, computational biology, Theoretical chemistry

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; 5) Bioinformatics; and 6) Protein engineering.
With the sequencing of the human genome and the genomes of thousands of species of interest, Structural Genomics (SG) projects have now reported 15,000 new protein structures. The next question is: What do these structures actually do? With support from the National Science Foundation, 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 (see Wang, Yin, et al. BMC Bioinformatics, 14, Suppl 3:S13, 2013) and GRASP-Func (Mills, Garg, et al. Protein Science 27, 1125-1135, 2018) methods use 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 Professor Penny Beuning to test and verify our predictions pertaining to multilayer active sites. This is a very important question for enzyme design.
With the many very active programs in Medicinal Chemistry in this Department, the Ondrechen group also provides computational collaboration for multiple different drug discovery efforts. One of our current projects, with Professors Agar and Manetsch and funded by the ALS Association, seeks a new therapeutic approach to amyotrophic lateral sclerosis. Another current project is identifying and characterizing druggable sites in proteins of SARS-COV-2, the novel coronavirus.

Mary Jo Ondrechen in the news


The Coronavirus Might Have Weak Spots. Machine Learning Could Help Find Them.

What makes SARS-CoV-2 so infectious? The answer is in its proteins. Mary Jo Ondrechen and Penny Beuning, professors of chemistry and chemical biology, are using machine learning to investigate these proteins and begin to understand how to slow the spread of the virus.

Collaborating to Fight Cancer with Knowledge

Researchers at Northeastern University and the Dana-Farber Cancer Institute have long recognized and taken advantage of the complementary strengths of the two institutions. “Our collaboration with Dana-Farber has been rich over the years,” said Stephen Zoloth, Northeastern’s dean of academic affairs for external programs and vice provost for health research. “But it has generally been […]