This profile is currently being updated. Some information may be incomplete.
Education
- B.S., Biochemistry, Grove City College, Grove City, PA
- Ph.D., Chemistry, Johns Hopkins University, Baltimore, MD
Research
Interests
- Bioorganic Chemistry
- Biomolecular Modeling of Carbohydrates and Post-Translational Modifications
Publications
- Nance, M.;Labonte, J.W.; Adolf-Bryfogle, J.; Gray, J.J. “Development and evaluation of GlycanDock: A protein–glycoligand docking algorithm in Rosetta.”J. Phys. Chem. B, 2021, 125, 6807–6820.
- 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.”The Biophysicist, 2021, 2, 108–122.
- Mahajan S.P.; Srinivasan, Y.;Labonte, J.W.; DeLisa, M.P.; Gray, J.J. “Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2.”ACS Catal. 2021, 11, 2977–2991.
- 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.”J. Chem. Educ. 2020, 98, 400–409.
- 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.”Proteins 2019, 1–13.
- 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.”ChemBioChem 2017, 18, 1204–1215.
- Labonte, J.W.; Adolf-Bryfogle, J.; Schief, W.R.; Gray, J.J. “Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures.”J. Comput. Chem. 2017, 38, 276–287.
- Labonte, J.W.& Townsend, C.A. “Active Site Comparisons and Catalytic Mechanisms of the Hot Dog Superfamily,”Chem. Rev. 2013, 113, 2182–2204.
- 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.)
Presentations
- Nance, M.;Labonte, J.W.; Adolf-Bryfogle, J.; Gray, J.J. “Development and evaluation of GlycanDock: A protein–glycoligand docking algorithm in Rosetta.”J. Phys. Chem. B, 2021, 125, 6807–6820.
- 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.”The Biophysicist, 2021, 2, 108–122.
- Mahajan S.P.; Srinivasan, Y.;Labonte, J.W.; DeLisa, M.P.; Gray, J.J. “Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2.”ACS Catal. 2021, 11, 2977–2991.
- 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.”J. Chem. Educ. 2020, 98, 400–409.
- 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.”Proteins 2019, 1–13.
- 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.”ChemBioChem 2017, 18, 1204–1215.
- Labonte, J.W.; Adolf-Bryfogle, J.; Schief, W.R.; Gray, J.J. “Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures.”J. Comput. Chem. 2017, 38, 276–287.
- Labonte, J.W.& Townsend, C.A. “Active Site Comparisons and Catalytic Mechanisms of the Hot Dog Superfamily,”Chem. Rev. 2013, 113, 2182–2204.
- 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
- Rosetta Commons
- Executive Board of theD2D CURE Network