The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
Alford, Rebecca F, Leaver-Fay, Andrew, Jeliazkov, Jeliazko R, O’Meara, Matthew J, DiMaio, Frank P, Park, Hahnbeom, Shapovalov, Maxim V, Renfrew, P. Douglas, Mulligan, Vikram K, Kappel, Kalli, Labonte, Jason W, Pacella, Michael S, Bonneau, Richard, Bradley, Philip, Dunbrack, Roland L, Das, Rhiju, Baker, David, Kuhlman, Brian, Kortemme, Tanja, Gray, Jeffrey J
Published in Journal of chemical theory and computation (13.06.2017)
Published in Journal of chemical theory and computation (13.06.2017)
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Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design
Adolf-Bryfogle, Jared, Labonte, Jason W, Kraft, John C, Shapovalov, Maxim, Raemisch, Sebastian, Lütteke, Thomas, DiMaio, Frank, Bahl, Christopher D, Pallesen, Jesper, King, Neil P, Gray, Jeffrey J, Kulp, Daniel W, Schief, William R
Published in PLoS computational biology (24.06.2024)
Published in PLoS computational biology (24.06.2024)
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Better together: Elements of successful scientific software development in a distributed collaborative community
Koehler Leman, Julia, Weitzner, Brian D, Renfrew, P Douglas, Lewis, Steven M, Moretti, Rocco, Watkins, Andrew M, Mulligan, Vikram Khipple, Lyskov, Sergey, Adolf-Bryfogle, Jared, Labonte, Jason W, Krys, Justyna, Bystroff, Christopher, Schief, William, Gront, Dominik, Schueler-Furman, Ora, Baker, David, Bradley, Philip, Dunbrack, Roland, Kortemme, Tanja, Leaver-Fay, Andrew, Strauss, Charlie E M, Meiler, Jens, Kuhlman, Brian, Gray, Jeffrey J, Bonneau, Richard
Published in PLoS computational biology (04.05.2020)
Published in PLoS computational biology (04.05.2020)
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Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization
Vagstad, Anna L, Hill, Eric A, Kamari-Bidkorpeh, Oliver, Korman, Tyler P, Townsend, Craig A, Crawford, Jason M, Tsai, Shiou-Chuan, Labonte, Jason W
Published in Nature (London) (22.10.2009)
Published in Nature (London) (22.10.2009)
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Structure and function of an iterative polyketide synthase thioesterase domain catalyzing Claisen cyclization in aflatoxin biosynthesis
Korman, Tyler Paz, Crawford, Jason M., Labonte, Jason W., Newman, Adam G., Wong, Justin, Townsend, Craig A., Tsai, Shiou-Chuan, Benkovic, Stephen J.
Published in Proceedings of the National Academy of Sciences - PNAS (06.04.2010)
Published in Proceedings of the National Academy of Sciences - PNAS (06.04.2010)
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Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design
Drew, Kevin, Renfrew, P Douglas, Craven, Timothy W, Butterfoss, Glenn L, Chou, Fang-Chieh, Lyskov, Sergey, Bullock, Brooke N, Watkins, Andrew, Labonte, Jason W, Pacella, Michael, Kilambi, Krishna Praneeth, Leaver-Fay, Andrew, Kuhlman, Brian, Gray, Jeffrey J, Bradley, Philip, Kirshenbaum, Kent, Arora, Paramjit S, Das, Rhiju, Bonneau, Richard
Published in PloS one (15.07.2013)
Published in PloS one (15.07.2013)
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A comprehensive, high-resolution map of a gene's fitness landscape
Firnberg, Elad, Labonte, Jason W, Gray, Jeffrey J, Ostermeier, Marc
Published in Molecular biology and evolution (01.06.2014)
Published in Molecular biology and evolution (01.06.2014)
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Autoproteolytic Activation of ThnT Results in Structural Reorganization Necessary for Substrate Binding and Catalysis
Buller, Andrew R., Labonte, Jason W., Freeman, Michael F., Wright, Nathan T., Schildbach, Joel F., Townsend, Craig A.
Published in Journal of molecular biology (28.09.2012)
Published in Journal of molecular biology (28.09.2012)
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Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1
Mulligan, Vikram Khipple, Workman, Sean, Sun, Tianjun, Rettie, Stephen, Li, Xinting, Worrall, Liam J, Craven, Timothy W, King, Dustin T, Hosseinzadeh, Parisa, Watkins, Andrew M, Renfrew, P Douglas, Guffy, Sharon, Labonte, Jason W, Moretti, Rocco, Bonneau, Richard, Strynadka, Natalie C J, Baker, David
Published in Proceedings of the National Academy of Sciences - PNAS (23.03.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (23.03.2021)
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Residue‐centric modeling and design of saccharide and glycoconjugate structures
Labonte, Jason W., Adolf‐Bryfogle, Jared, Schief, William R., Gray, Jeffrey J.
Published in Journal of computational chemistry (15.02.2017)
Published in Journal of computational chemistry (15.02.2017)
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Structural Basis for Peptide Substrate Specificities of Glycosyltransferase GalNAc-T2
Mahajan, Sai Pooja, Srinivasan, Yashes, Labonte, Jason W, DeLisa, Matthew P, Gray, Jeffrey J
Published in ACS catalysis (05.03.2021)
Published in ACS catalysis (05.03.2021)
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Shotgun scanning glycomutagenesis: A simple and efficient strategy for constructing and characterizing neoglycoproteins
Li, Mingji, Zheng, Xiaolu, Shanker, Sudhanshu, Jaroentomeechai, Thapakorn, Moeller, Tyler D., Hulbert, Sophia W., Koçer, Ilkay, Byrne, Josef, Cox, Emily C., Fu, Qin, Zhang, Sheng, Labonte, Jason W., Gray, Jeffrey J., DeLisa, Matthew P.
Published in Proceedings of the National Academy of Sciences - PNAS (28.09.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (28.09.2021)
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Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter
Piepenbrink, Kurt H., Lillehoj, Erik, Harding, Christian M., Labonte, Jason W., Zuo, Xiaotong, Rapp, Chelsea A., Munson, Robert S., Goldblum, Simeon E., Feldman, Mario F., Gray, Jeffrey J., Sundberg, Eric J.
Published in The Journal of biological chemistry (28.10.2016)
Published in The Journal of biological chemistry (28.10.2016)
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Computational design of mixed chirality peptide macrocycles with internal symmetry
Mulligan, Vikram Khipple, Kang, Christine S., Sawaya, Michael R., Rettie, Stephen, Li, Xinting, Antselovich, Inna, Craven, Timothy W., Watkins, Andrew M., Labonte, Jason W., DiMaio, Frank, Yeates, Todd O., Baker, David
Published in Protein science (01.12.2020)
Published in Protein science (01.12.2020)
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A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape
Firnberg, Elad, Labonte, Jason W, Gray, Jeffrey J, Ostermeier, Marc
Published in Molecular biology and evolution (01.05.2016)
Published in Molecular biology and evolution (01.05.2016)
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Development of a Broadly Accessible, Computationally Guided Biochemistry Course-Based Undergraduate Research Experience
Vater, Ashley, Mayoral, Jaime, Nunez-Castilla, Janelle, Labonte, Jason W, Briggs, Laura A, Gray, Jeffrey J, Makarevitch, Irina, Rumjahn, Sharif M, Siegel, Justin B
Published in Journal of chemical education (09.02.2021)
Published in Journal of chemical education (09.02.2021)
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Novel sampling strategies and a coarse‐grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37–45
Roy Burman, Shourya S., Nance, Morgan L., Jeliazkov, Jeliazko R., Labonte, Jason W., Lubin, Joseph H., Biswas, Naireeta, Gray, Jeffrey J.
Published in Proteins, structure, function, and bioinformatics (01.08.2020)
Published in Proteins, structure, function, and bioinformatics (01.08.2020)
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Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
Koehler Leman, Julia, Lyskov, Sergey, Lewis, Steven M, Adolf-Bryfogle, Jared, Alford, Rebecca F, Barlow, Kyle, Ben-Aharon, Ziv, Farrell, Daniel, Fell, Jason, Hansen, William A, Harmalkar, Ameya, Jeliazkov, Jeliazko, Kuenze, Georg, Krys, Justyna D, Ljubetič, Ajasja, Loshbaugh, Amanda L, Maguire, Jack, Moretti, Rocco, Mulligan, Vikram Khipple, Nance, Morgan L, Nguyen, Phuong T, Ó Conchúir, Shane, Roy Burman, Shourya S, Samanta, Rituparna, Smith, Shannon T, Teets, Frank, Tiemann, Johanna K S, Watkins, Andrew, Woods, Hope, Yachnin, Brahm J, Bahl, Christopher D, Bailey-Kellogg, Chris, Baker, David, Das, Rhiju, DiMaio, Frank, Khare, Sagar D, Kortemme, Tanja, Labonte, Jason W, Lindorff-Larsen, Kresten, Meiler, Jens, Schief, William, Schueler-Furman, Ora, Siegel, Justin B, Stein, Amelie, Yarov-Yarovoy, Vladimir, Kuhlman, Brian, Leaver-Fay, Andrew, Gront, Dominik, Gray, Jeffrey J, Bonneau, Richard
Published in Nature communications (29.11.2021)
Published in Nature communications (29.11.2021)
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