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Jason W. Labonte, Ph.D. - Publications

Affiliations: 
2011 Johns Hopkins University, Baltimore, MD 
Area:
Organic and Bioorganic Chemistry
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, et al. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockville, Md.). 2: 108-122. PMID 35128343 DOI: 10.35459/tbp.2019.000147  0.721
2021 Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, ... ... Labonte JW, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7  0.368
2021 Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, et al. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33723038 DOI: 10.1073/pnas.2012800118  0.339
2020 Mulligan VK, Kang CS, Sawaya MR, Rettie S, Li X, Antselovich I, Craven TW, Watkins AM, Labonte JW, DiMaio F, Yeates TO, Baker D. Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Science : a Publication of the Protein Society. PMID 33058266 DOI: 10.1002/pro.3974  0.349
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Labonte JW, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.725
2020 Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507  0.759
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009  0.729
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008  0.737
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007  0.732
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005  0.719
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004  0.725
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003  0.745
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002  0.73
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001  0.721
2019 Roy Burman SS, Nance ML, Jeliazkov JR, Labonte JW, Lubin JH, Biswas N, Gray JJ. Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI Rounds 37-45. Proteins. PMID 31742764 DOI: 10.1002/Prot.25855  0.543
2019 Srinivasan Y, Pooja Mahajan S, Labonte J, DeLisa MP, Gray JJ. Structure-Based Prediction of Polypeptide Substrate Specificities of Glycosyltransferases Biophysical Journal. 116: 68a. DOI: 10.1016/J.Bpj.2018.11.410  0.536
2017 Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125  0.584
2017 Mathew M, Tan E, Labonte JW, Shah S, Saeui CT, Liu L, Bhattacharya R, Bovonratwet P, Gray JJ, Yarema K. GLYCOENGINEERING OF ESTERASE ACTIVITY THROUGH METABOLIC FLUX-BASED MODULATION OF SIALIC ACID. Chembiochem : a European Journal of Chemical Biology. PMID 28218815 DOI: 10.1002/Cbic.201600698  0.521
2016 Labonte JW, Adolf-Bryfogle J, Schief WR, Gray JJ. Residue-centric modeling and design of saccharide and glycoconjugate structures. Journal of Computational Chemistry. PMID 27900782 DOI: 10.1002/Jcc.24679  0.583
2016 Piepenbrink KJ, Lillehoj EP, Harding CM, Labonte JW, Zuo X, Rapp CA, Munson RS, Goldblum SE, Feldman MF, Gray JJ, Sundberg EJ. Structural diversity in the type IV pili of multidrug-resistant Acinetobacter. The Journal of Biological Chemistry. PMID 27634041 DOI: 10.1074/Jbc.M116.751099  0.508
2016 Firnberg E, Labonte JW, Gray JJ, Ostermeier M. A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape. Molecular Biology and Evolution. PMID 26912810 DOI: 10.1093/Molbev/Msw021  0.457
2015 Pierre B, Labonte JW, Xiong T, Aoraha E, Williams A, Shah V, Chau E, Helal KY, Gray JJ, Kim JR. Molecular Determinants for Protein Stabilization by Insertional Fusion to a Thermophilic Host Protein. Chembiochem : a European Journal of Chemical Biology. PMID 26391210 DOI: 10.1002/Cbic.201500310  0.503
2015 Labonte JW, Gray JJ. Docking and Design of Oligosaccharides, Glycoproteins, and Glycolipids Biophysical Journal. 108: 470a. DOI: 10.1016/J.Bpj.2014.11.2568  0.592
2014 Firnberg E, Labonte JW, Gray JJ, Ostermeier M. A comprehensive, high-resolution map of a gene's fitness landscape. Molecular Biology and Evolution. 31: 1581-92. PMID 24567513 DOI: 10.1093/Molbev/Msu081  0.487
2013 Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ. Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins. 81: 2201-9. PMID 24123494 DOI: 10.1002/Prot.24425  0.754
2013 Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, et al. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Plos One. 8: e67051. PMID 23869206 DOI: 10.1371/Journal.Pone.0067051  0.771
2013 Labonte JW, Townsend CA. Active site comparisons and catalytic mechanisms of the hot dog superfamily. Chemical Reviews. 113: 2182-204. PMID 23205964 DOI: 10.1021/Cr300169A  0.539
2012 Labonte JW, Kudo F, Freeman MF, Raber ML, Townsend CA. Engineering the synthetic potential of β-lactam synthetase and the importance of catalytic loop dynamics. Medchemcomm. 3: 960-966. PMID 23616913 DOI: 10.1039/C2Md00305H  0.706
2012 Vagstad AL, Hill EA, Labonte JW, Townsend CA. Characterization of a fungal thioesterase having Claisen cyclase and deacetylase activities in melanin biosynthesis. Chemistry & Biology. 19: 1525-34. PMID 23261597 DOI: 10.1016/j.chembiol.2012.10.002  0.749
2012 Buller AR, Labonte JW, Freeman MF, Wright NT, Schildbach JF, Townsend CA. Autoproteolytic activation of ThnT results in structural reorganization necessary for substrate binding and catalysis. Journal of Molecular Biology. 422: 508-18. PMID 22706025 DOI: 10.1016/J.Jmb.2012.06.012  0.764
2010 Korman TP, Crawford JM, Labonte JW, Newman AG, Wong J, Townsend CA, Tsai SC. Structure and function of an iterative polyketide synthase thioesterase domain catalyzing Claisen cyclization in aflatoxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 107: 6246-51. PMID 20332208 DOI: 10.1073/Pnas.0913531107  0.656
2009 Crawford JM, Korman TP, Labonte JW, Vagstad AL, Hill EA, Kamari-Bidkorpeh O, Tsai SC, Townsend CA. Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization. Nature. 461: 1139-43. PMID 19847268 DOI: 10.1038/Nature08475  0.748
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