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Chemistry Department

Education

• B.S., Biochemistry, Grove City College, Grove City, PA
• Ph.D., Chemistry, Johns Hopkins University, Baltimore, MD

Bio

Professor Labonte earned his Ph.D. in Bioorganic Chemistry from Johns Hopkins University in Baltimore, Maryland, under Craig Townsend, studying the mechanisms of megasynthase enzymes. He then worked as a postdoctoral fellow for Jeffrey Gray in Biomolecular Engineering at Johns Hopkins, developing computer algorithms for modeling carbohydrate structures with the Rosetta modeling and design suite. His current research continues to expand the carbohydrate modeling tools that he developed as a postdoctoral fellow, including the addition of glycoengineering and design tools. Labonte is an avid backpacker and hopes to complete the entire Appalachian Trail.

Research Interests

Bioorganic Chemistry
Biomolecular Modeling of Carbohydrates and Post-Translational Modifications

Recent Publications and Presentations

• Nance, M.; Labonte, J.W.; Adolf-Bryfogle, J.; Gray, J.J. “Development and evaluation of GlycanDock: A protein–glycoligand docking algorithm in Rosetta.”
• Le, K.H.; Adolf-Bryfogle, J.; Klima, J.C.; Lyskov, S.; Labonte, J.W.; Bertolani, S.; Roy Burman, S.S.; Leaver-Fay, A., Weitzner, B.D.; Maguire, J.; Rangan, R.; Adrianowycz, M.A.; Alford, R.F.; Adal, A.; Nance, M.L.; Wu, Y.; Willis, J.; Kulp, D.W.; Das, R.; Dunbrack, R.L. Jr.; Schief, W.; Kuhlman, B.; Siegel, J.B.; Gray, J.J. “PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.”
• Mahajan S.P.; Srinivasan, Y.; Labonte, J.W.; DeLisa, M.P.; Gray, J.J. “Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2.”
• Vater, A.; Mayoral, J.; Nunez-Castilla, J.; Labonte, J.W.; Briggs, L.A.; Gray, J.J.; Makarevitch, I.; Rumjahn, S.M.; Siegel, J.B. “Development of a Broadly Accessible, Computationally Guided Biochemistry Course-Based Undergraduate Research Experience.”
• Roy Burman, S.S.; Nance, M.L.; Jeliazkov, J.R.; Labonte, J.W.; Lubin, J.H.; Biswas, N.; Gray, J.J. “Novel Sampling Strategies and a Coarse‐Grained Score Function for Docking Homomers, Flexible Heteromers, and Oligosaccharides Using Rosetta in CAPRI Rounds 37–45.”
• Mathew, M.P.; Tan, E.; Labonte, J.W.; Shaw, S.; Saeui, C.T.; Liu, L.; Bhattacharya, R.; Bovonratwet, P.; Gray, J.J.; Yarema, K.J. “Glycoengineering of Esterase Activity Through Metabolic Flux-Based Modulation of Sialic Acid.”
• Labonte, J.W.; Adolf-Bryfogle, J.; Schief, W.R.; Gray, J.J. “Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures.”
• Labonte, J.W. & Townsend, C.A. “Active Site Comparisons and Catalytic Mechanisms of the Hot Dog Superfamily,”  
• Koehler Leman, J.; Lyskov, S.; Lewis, S.; Adolf-Bryfogle, J.; Alford, R.F.; Barlow, K; Ben-Aharon, Z.; Farrell, D.; Fell, J.; Hansen, W.A.; Harmalkar, A.; Jeliazkov, J.; Kuenze, G.; Krys, J.D.; Ljubetič, A.; Loshbaugh, A.L.; Maguire, J.; Moretti, R.; Mulligan, V.K.; Nguyen, P.T.; Ó Conchúir, S.; Roy Burman, S.S.; Smith, S.T.; Teets, F.; Tiemann, J.K.S.; Watkins, A.; Woods, H.; Yachnin, B.J.; Bahl, C.D.; Bailey- Kellogg, C.; Baker, D.; Das, R.; DiMaio, F.; Khare, S.D.; Kortemme, T.; Labonte, J.W.; Lindorff-Larsen, K.; Meiler, J.; Schief, W.; Schueler-Furman, O.; Siegel, J.; Stein, A.; Yarov-Yarovoy, V.; Kuhlman, B.; Leaver-Fay, A.; Gront, D.; Gray, J.J.; Bonneau, R. “Ensuring scientific reproducibility in bio- macromolecular modeling via extensive, automated benchmarks.” Nat. Commun., 2021, 12, 6947. Li, M.; Zheng, X.; Shanker, S.; Jaroentomeechai, T.; Moeller, T.D.; Hulbert, S.W.; Kocer, I.; Byrne, J.; Cox, E.; Fu, Q.; Zhang, S.; Labonte, J.W.; Gray, J.J.; DeLisa, M.P. “Shotgun scanning glycomutagenesis: a simple and efficient strategy for constructing and characterizing neoglycoproteins.” Proc. Natl. Acad. Sci., 2021, 118, e2107440118. Mulligan, V.K.; Workman, S.D.; Sun, T.; Rettie, S.; Li, X.; Worrall, L.J.; Craven, T.; King, D.T.; Hosseinzadeh, P.; Watkins, A.; Renfrew, P.D.; Guffy, S.; Labonte, J.W.; Moretti, R.; Bonneau, R.; Strynadka, N.C.J.; Baker, D. “Computationally-designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1.” Proc. Natl. Acad. Sci. 2021, 118, e2012800118. (Also, the journal names and the issue numbers in the HTML on this part of the page should be italicized, and the years should be bolded.)

Professional Affiliations & Memberships

• Executive Board of the