Zobrazeno 1 - 10
of 15
pro vyhledávání: '"Kyle A. Barlow"'
Autor:
David Mavor, Kyle A. Barlow, Daniel Asarnow, Yuliya Birman, Derek Britain, Weilin Chen, Evan M. Green, Lillian R. Kenner, Bruk Mensa, Leanna S. Morinishi, Charlotte A. Nelson, Erin M. Poss, Pooja Suresh, Ruilin Tian, Taylor Arhar, Beatrice E. Ary, David P. Bauer, Ian D. Bergman, Rachel M. Brunetti, Cynthia M. Chio, Shizhong A. Dai, Miles S. Dickinson, Susanna K. Elledge, Cole V. M. Helsell, Nathan L. Hendel, Emily Kang, Nadja Kern, Matvei S. Khoroshkin, Lisa L. Kirkemo, Greyson R. Lewis, Kevin Lou, Wesley M. Marin, Alison M. Maxwell, Peter F. McTigue, Douglas Myers-Turnbull, Tamas L. Nagy, Andrew M. Natale, Keely Oltion, Sergei Pourmal, Gabriel K. Reder, Nicholas J. Rettko, Peter J. Rohweder, Daniel M. C Schwarz, Sophia K. Tan, Paul V. Thomas, Ryan W. Tibble, Jason P. Town, Mary K. Tsai, Fatima S. Ugur, Douglas R. Wassarman, Alexander M. Wolff, Taia S. Wu, Derek Bogdanoff, Jennifer Li, Kurt S. Thorn, Shane O'Conchúir, Danielle L. Swaney, Eric D. Chow, Hiten D. Madhani, Sy Redding, Daniel N. Bolon, Tanja Kortemme, Joseph L. DeRisi, Martin Kampmann, James S. Fraser
Publikováno v:
Biology Open, Vol 7, Iss 7 (2018)
Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the di
Externí odkaz:
https://doaj.org/article/120375a9425d4b15800ba82e59af4543
Autor:
Shane Ó Conchúir, Kyle A Barlow, Roland A Pache, Noah Ollikainen, Kale Kundert, Matthew J O'Meara, Colin A Smith, Tanja Kortemme
Publikováno v:
PLoS ONE, Vol 10, Iss 9, p e0130433 (2015)
The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse bi
Externí odkaz:
https://doaj.org/article/1f949fb55f484b8db27a3fc860f872d1
Autor:
Dominik Gront, Kresten Lindorff-Larsen, Jack Maguire, Jens Meiler, Christopher D. Bahl, Jason S. Fell, Chris Bailey-Kellogg, Andrew M. Watkins, Frank DiMaio, Daniel P. Farrell, Jared Adolf-Bryfogle, Julia Koehler Leman, Frank D. Teets, Vladimir Yarov-Yarovoy, Ajasja Ljubetič, Shannon T. Smith, William A. Hansen, Steven M. Lewis, Justyna Krys, Shourya S. Roy Burman, Amelie Stein, Rhiju Das, David Baker, Vikram Khipple Mulligan, Jason W. Labonte, Georg Kuenze, William R. Schief, Rebecca F. Alford, Shane Ó Conchúir, Hope Woods, Tanja Kortemme, Johanna K. S. Tiemann, Sagar D. Khare, Sergey Lyskov, Ziv Ben-Aharon, Ora Schueler-Furman, Amanda L. Loshbaugh, Richard Bonneau, Brahm J. Yachnin, Andrew Leaver-Fay, Kyle A. Barlow, Phuong T. Nguyen, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Justin B. Siegel, Rocco Moretti, Ameya Harmalkar, Brian Kuhlman
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and comp
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7ae3b538a88ca76a15e111345bd76765
https://doi.org/10.1101/2021.04.04.438423
https://doi.org/10.1101/2021.04.04.438423
Autor:
Tushar Jain, Todd Boland, Yingda Xu, Arvind Sivasubramanian, Xiaojun Lu, Kyle A. Barlow, R. Paul Nobrega, Maximiliano Vásquez, Heather Lynaugh
Publikováno v:
mAbs
Contemporary in vivo and in vitro discovery platform technologies greatly increase the odds of identifying high-affinity monoclonal antibodies (mAbs) towards essentially any desired biologically relevant epitope. Lagging discovery throughput is the a
Autor:
Michael C. Thompson, Tanja Kortemme, Daniel J. Mandell, Kyle A. Barlow, Jenna Pellegrino, Yao-Ming Huang, James S. Fraser, Amanda L. Loshbaugh, Anum A. Glasgow, Noah Ollikainen, Mark J. S. Kelly, Ryan Ritterson, Cody Krivacic, Deborah Jeon, Roland A. Pache
Publikováno v:
Science
Science (New York, N.Y.), vol 366, iss 6468
Science (New York, N.Y.), vol 366, iss 6468
Sense and respond Many signaling pathways start with cellular proteins sensing and responding to small molecules. Despite advances in protein design, creating a protein-based sense-and-respond system remains challenging. Glasgow et al. designed bindi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf3b5ab92ce33debbe89d63e90254e35
https://europepmc.org/articles/PMC7343396/
https://europepmc.org/articles/PMC7343396/
Autor:
Jack Maguire, Ragul Gowthaman, Marion F. Sauer, Georg Kuenze, Tanja Kortemme, Benjamin Basanta, Indigo Chris King, Jens Meiler, Rhiju Das, Ora Schueler-Furman, Nicholas A. Marze, Brandon Frenz, Christoffer Norn, Julia Koehler Leman, Jason W. Labonte, Kala Bharath Pilla, Lei Shi, Sergey Lyskov, Brian D. Weitzner, Nir London, Karen R. Khar, Jaume Bonet, Nawsad Alam, Andreas Scheck, Alexander M. Sevy, Lars Malmström, Thomas Huber, Christopher Bystroff, Lior Zimmerman, Lorna Dsilva, Bruno E. Correia, Roland L. Dunbrack, Sergey Ovchinnikov, Rocco Moretti, Scott Horowitz, Phil Bradley, Frank DiMaio, Noah Ollikainen, Brian Kuhlman, Jeffrey J. Gray, Melanie L. Aprahamian, Andrew Leaver-Fay, Santrupti Nerli, Brian Koepnick, Xingjie Pan, Manasi A. Pethe, Andrew M. Watkins, Summer B. Thyme, Enrique Marcos, Vikram Khipple Mulligan, Hahnbeom Park, Po-Ssu Huang, David K. Johnson, Daniel-Adriano Silva, Patrick Barth, Shannon Smith, Caleb Geniesse, Jason K. Lai, Patrick Conway, Amelie Stein, Jeliazko R. Jeliazkov, David Baker, Dominik Gront, Kalli Kappel, Firas Khatib, Robert Kleffner, Brian J. Bender, Richard Bonneau, Kyle A. Barlow, Joseph H. Lubin, Shourya S. Roy Burman, Nikolaos G. Sgourakis, Yuval Sedan, Ryan E. Pavlovicz, Kristin Blacklock, Seth Cooper, Barak Raveh, Alisa Khramushin, John Karanicolas, Justin B. Siegel, Sharon L. Guffy, Brian G. Pierce, Alex Ford, Darwin Y. Fu, Orly Marcu, Gideon Lapidoth, Brian Coventry, René M. de Jong, Shane O’Conchúir, Thomas W. Linsky, William R. Schief, Rebecca F. Alford, Scott E. Boyken, Sagar D. Khare, Maria Szegedy, Ray Yu-Ruei Wang, Steven M. Lewis, Hamed Khakzad, Timothy M. Jacobs, Frank D. Teets, Lukasz Goldschmidt, Daisuke Kuroda, Steffen Lindert, P. Douglas Renfrew, Yifan Song, Jared Adolf-Bryfogle, Michael S. Pacella, Aliza B. Rubenstein
Publikováno v:
Nat Methods
The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactore
Autor:
Danielle L. Swaney, Alexander M. Wolff, Tamas L. Nagy, Douglas Myers-Turnbull, Douglas R. Wassarman, Kyle A. Barlow, Paul V. Thomas, Rachel M. Brunetti, Derek Britain, Kevin Lou, Sy Redding, Wesley M. Marin, Mary K. Tsai, Kurt S. Thorn, Ryan W. Tibble, Lillian R. Kenner, Daniel M. C. Schwarz, Charlotte A. Nelson, Bruk Mensa, Fatima S. Ugur, Derek Bogdanoff, Taia S. Wu, E. Kang, Nicholas J. Rettko, Leanna S. Morinishi, Peter F. McTigue, Martin Kampmann, Gabriel K. Reder, Eric D. Chow, Alison M Maxwell, Jason Town, James S. Fraser, Andrew M. Natale, David P. Bauer, Cole Helsell, Joseph L. DeRisi, Yuliya Birman, Pooja Suresh, Evan M. Green, Ruilin Tian, Jennifer Y. Li, Sergei Pourmal, Weilin Chen, Hiten D. Madhani, Daniel N. Bolon, Miles Sasha Dickinson, Shane O’Conchúir, Keely Oltion, Daniel Asarnow, Peter J. Rohweder, Susanna K. Elledge, David Mavor, Erin M. Poss, Matvei S. Khoroshkin, Beatrice Ary, Ian D. Bergman, Nadja Kern, Taylor Arhar, Lisa L. Kirkemo, Tanja Kortemme, Sophia K. Tan, Shizhong Dai, Greyson R. Lewis, Nathan L. Hendel, Cynthia M. Chio
Publikováno v:
Biology Open
Biology open, vol 7, iss 7
Biology Open, Vol 7, Iss 7 (2018)
Mavor, D; Barlow, KA; Asarnow, D; Birman, Y; Britain, D; Chen, W; et al.(2018). Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. BIOLOGY OPEN, 7(7). doi: 10.1242/bio.036103. UCSF: Retrieved from: http://www.escholarship.org/uc/item/2hz894gr
Biology open, vol 7, iss 7
Biology Open, Vol 7, Iss 7 (2018)
Mavor, D; Barlow, KA; Asarnow, D; Birman, Y; Britain, D; Chen, W; et al.(2018). Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. BIOLOGY OPEN, 7(7). doi: 10.1242/bio.036103. UCSF: Retrieved from: http://www.escholarship.org/uc/item/2hz894gr
Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the di
Autor:
James E. Lucas, Pooja Suresh, Tanja Kortemme, Kyle A. Barlow, Shane Ó Conchúir, Samuel Thompson, Markus Heinonen
Computationally modeling changes in binding free energies upon mutation (interface ΔΔG) allows large-scale prediction and perturbation of protein-protein interactions. Additionally, methods that consider and sample relevant conformational plasticit
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d361bb5f3714300a90235e9bc29216e5
https://europepmc.org/articles/PMC5980710/
https://europepmc.org/articles/PMC5980710/
Autor:
Nadja Kern, Taylor Arhar, Matvei S. Khoroshkin, Ian D. Bergman, Lisa L. Kirkemo, Danielle L. Swaney, Nathan L. Hendel, Jason Town, Weilin Chen, Lillian R. Kenner, Alexander M. Wolff, Wesley M. Marin, Rachel M. Brunetti, Charlotte A. Nelson, Susanna K. Elledge, Sergei Pourmal, Greyson R. Lewis, Cynthia M. Chio, Derek Britain, Derrick Bogdanoff, Andrew M. Natale, Shane O’Conchúir, Martin Kampmann, Douglas R. Wassarmann, Kyle A. Barlow, Bruk Mensa, Gabriel K. Reder, Kurt S. Thorn, Ryan W. Tibble, Pooja Suresh, Sy Redding, Keely Oltion, Tanja Kortemme, James S. Fraser, Daniel Asarnow, Evan M. Green, Fatima S. Ugur, David L.V. Bauer, Sophia K. Tan, Joseph L. DeRisi, Beatrice Ary, Yuliya Birman, Tamas L. Nagy, Daniel N. Bolon, Miles Sasha Dickinson, Taia Wu, K. Tsai, Peter F. McTigue, Ruilin Tian, Nicholas J. Rettko, Shizhong Dai, Hiten D. Madhani, Jennifer Y. Li, Douglas Myers-Turnbull, Kevin Lou, Peter J. Rohweder, David Mavor, Daniel M. C. Schwarz, Alison M Maxwell, Erin M. Poss, Cole Helsell, E. Kang, Leanna S. Morinishi, Paul Thomas, Eric D. Chow
Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the di
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::beb1693458a8341e04b43f423acafd0d
Publikováno v:
Methods in Molecular Biology ISBN: 9781493935673
In recent years, interest in controlling protein function with light has increased. Light offers a number of unique advantages over other methods, including spatial and temporal control and high selectivity. Here, we describe a general protocol for e