Search Results - "Labonte, Jason W"

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design by 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

“…Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation…”
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Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta by Nance, Morgan L, Labonte, Jason W, Adolf-Bryfogle, Jared, Gray, Jeffrey J

“…Carbohydrate chains are ubiquitous in the complex molecular processes of life. These highly diverse chains are recognized by a variety of protein receptors,…”
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Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design by 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

“…Carbohydrates and glycoproteins modulate key biological functions. However, experimental structure determination of sugar polymers is notoriously difficult…”
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Better together: Elements of successful scientific software development in a distributed collaborative community by 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

“…Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished…”
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Active Site Comparisons and Catalytic Mechanisms of the Hot Dog Superfamily by Labonte, Jason W, Townsend, Craig A

“…A study investigated the active site comparisons and catalytic mechanisms of a long hot dog helix. Data indicate that the hot dog fold is a useful and…”
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Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization by Vagstad, Anna L, Hill, Eric A, Kamari-Bidkorpeh, Oliver, Korman, Tyler P, Townsend, Craig A, Crawford, Jason M, Tsai, Shiou-Chuan, Labonte, Jason W

“…Polyketides are a class of natural products with diverse structures and biological activities. The structural variability of aromatic products of fungal…”
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Structure and function of an iterative polyketide synthase thioesterase domain catalyzing Claisen cyclization in aflatoxin biosynthesis by Korman, Tyler Paz, Crawford, Jason M., Labonte, Jason W., Newman, Adam G., Wong, Justin, Townsend, Craig A., Tsai, Shiou-Chuan, Benkovic, Stephen J.

“…Polyketide natural products possess diverse architectures and biological functions and share a subset of biosynthetic steps with fatty acid synthesis. The…”
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Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design by 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

“…Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be…”
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A comprehensive, high-resolution map of a gene's fitness landscape by Firnberg, Elad, Labonte, Jason W, Gray, Jeffrey J, Ostermeier, Marc

“…Mutations are central to evolution, providing the genetic variation upon which selection acts. A mutation's effect on the suitability of a gene to perform a…”
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Autoproteolytic Activation of ThnT Results in Structural Reorganization Necessary for Substrate Binding and Catalysis by Buller, Andrew R., Labonte, Jason W., Freeman, Michael F., Wright, Nathan T., Schildbach, Joel F., Townsend, Craig A.

“…cis-Autoproteolysis is a post-translational modification necessary for the function of ThnT, an enzyme involved in the biosynthesis of the β-lactam antibiotic…”
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Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1 by 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

“…The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial…”
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Residue‐centric modeling and design of saccharide and glycoconjugate structures by Labonte, Jason W., Adolf‐Bryfogle, Jared, Schief, William R., Gray, Jeffrey J.

“…The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development…”
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Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter by 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.

“…Acinetobacter baumannii is a Gram-negative coccobacillus found primarily in hospital settings that has recently emerged as a source of hospital-acquired…”
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Structural Basis for Peptide Substrate Specificities of Glycosyltransferase GalNAc-T2 by Mahajan, Sai Pooja, Srinivasan, Yashes, Labonte, Jason W, DeLisa, Matthew P, Gray, Jeffrey J

“…The polypeptide N-acetylgalactosaminyl transferase (GalNAc-T) enzyme family initiates O-linked mucin-type glycosylation. The family constitutes 20 isoenzymes…”
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Shotgun scanning glycomutagenesis: A simple and efficient strategy for constructing and characterizing neoglycoproteins by 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.

“…As a common protein modification, asparagine-linked (N-linked) glycosylation has the capacity to greatly influence the biological and biophysical properties of…”
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Computational design of mixed chirality peptide macrocycles with internal symmetry by 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

“…Cyclic symmetry is frequent in protein and peptide homo‐oligomers, but extremely rare within a single chain, as it is not compatible with free N‐ and…”
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A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape by Firnberg, Elad, Labonte, Jason W, Gray, Jeffrey J, Ostermeier, Marc

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Development of a Broadly Accessible, Computationally Guided Biochemistry Course-Based Undergraduate Research Experience by Vater, Ashley, Mayoral, Jaime, Nunez-Castilla, Janelle, Labonte, Jason W, Briggs, Laura A, Gray, Jeffrey J, Makarevitch, Irina, Rumjahn, Sharif M, Siegel, Justin B

“…Including undergraduate research in STEM education is a well-supported and growing high-impact practice that has been made much more scalable through…”
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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 by Roy Burman, Shourya S., Nance, Morgan L., Jeliazkov, Jeliazko R., Labonte, Jason W., Lubin, Joseph H., Biswas, Naireeta, Gray, Jeffrey J.

“…Critical Assessment of PRediction of Interactions (CAPRI) rounds 37 through 45 introduced larger complexes, new macromolecules, and multistage assemblies. For…”
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Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks by 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

“…Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering…”
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