J
Justin B. Siegel
Researcher at University of California, Davis
Publications - 96
Citations - 3094
Justin B. Siegel is an academic researcher from University of California, Davis. The author has contributed to research in topics: Medicine & Chemistry. The author has an hindex of 19, co-authored 77 publications receiving 2249 citations. Previous affiliations of Justin B. Siegel include University of California, Berkeley & University of Washington.
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Journal ArticleDOI
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
Justin B. Siegel,Alexandre Zanghellini,Helena M. Lovick,Gert Kiss,Abigail R. Lambert,Jennifer L. St.Clair,Jasmine L. Gallaher,Donald Hilvert,Michael H. Gelb,Barry L. Stoddard,Kendall N. Houk,Forrest E. Michael,David Baker +12 more
TL;DR: The design of enzymes that catalyze the bimolecular Diels-Alder reaction, a carbon-carbon bond formation reaction that is central to organic synthesis but unknown in natural metabolism, is described.
Journal ArticleDOI
Macromolecular modeling and design in Rosetta: recent methods and frameworks
Julia Koehler Leman,Brian D. Weitzner,Brian D. Weitzner,Steven M. Lewis,Steven M. Lewis,Jared Adolf-Bryfogle,Nawsad Alam,Rebecca F. Alford,Melanie L. Aprahamian,David Baker,Kyle A. Barlow,Patrick Barth,Patrick Barth,Benjamin Basanta,Brian J. Bender,Kristin Blacklock,Jaume Bonet,Jaume Bonet,Scott E. Boyken,Phil Bradley,Christopher Bystroff,Patrick Conway,Seth Cooper,Bruno E. Correia,Bruno E. Correia,Brian Coventry,Rhiju Das,René M. de Jong,Frank DiMaio,Lorna Dsilva,Roland L. Dunbrack,Alex Ford,Brandon Frenz,Darwin Y. Fu,Caleb Geniesse,Lukasz Goldschmidt,Ragul Gowthaman,Jeffrey J. Gray,Dominik Gront,Sharon L. Guffy,Scott Horowitz,Po-Ssu Huang,Thomas Huber,Timothy M. Jacobs,Jeliazko R. Jeliazkov,David K. Johnson,Kalli Kappel,John Karanicolas,Hamed Khakzad,Hamed Khakzad,Karen R. Khar,Sagar D. Khare,Firas Khatib,Alisa Khramushin,Indigo Chris King,Robert Kleffner,Brian Koepnick,Tanja Kortemme,Georg Kuenze,Brian Kuhlman,Daisuke Kuroda,Jason W. Labonte,Jason W. Labonte,Jason K. Lai,Gideon Lapidoth,Andrew Leaver-Fay,Steffen Lindert,Thomas W. Linsky,Nir London,Joseph H. Lubin,Sergey Lyskov,Jack Maguire,Lars Malmström,Lars Malmström,Lars Malmström,Enrique Marcos,Orly Marcu,Nicholas A. Marze,Jens Meiler,Rocco Moretti,Vikram Khipple Mulligan,Santrupti Nerli,Christoffer Norn,Shane O’Conchúir,Noah Ollikainen,Sergey Ovchinnikov,Michael S. Pacella,Xingjie Pan,Hahnbeom Park,Ryan E. Pavlovicz,Manasi A. Pethe,Brian G. Pierce,Kala Bharath Pilla,Barak Raveh,P. Douglas Renfrew,Shourya S. Roy Burman,Aliza B. Rubenstein,Marion F. Sauer,Andreas Scheck,Andreas Scheck,William R. Schief,Ora Schueler-Furman,Yuval Sedan,Alexander M. Sevy,Nikolaos G. Sgourakis,Lei Shi,Justin B. Siegel,Daniel-Adriano Silva,Shannon Smith,Yifan Song,Amelie Stein,Maria Szegedy,Frank D. Teets,Summer B. Thyme,Ray Yu-Ruei Wang,Andrew M. Watkins,Lior Zimmerman,Richard Bonneau +117 more
TL;DR: This Perspective reviews tools developed over the past five years in the Rosetta software, including over 80 methods, and discusses improvements to the score function, user interfaces and usability.
Journal ArticleDOI
Increased Diels-Alderase activity through backbone remodeling guided by Foldit players
Christopher B. Eiben,Justin B. Siegel,Jacob B. Bale,Seth Cooper,Firas Khatib,Betty W. Shen,Foldit Players,Barry L. Stoddard,Zoran Popović,David Baker +9 more
TL;DR: The use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure is reported, demonstrating that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems.
Journal ArticleDOI
Computational protein design enables a novel one-carbon assimilation pathway
Justin B. Siegel,Amanda L. Smith,Sean Poust,Adam J. Wargacki,Arren Bar-Even,Catherine Louw,Betty W. Shen,Christopher B. Eiben,Huu M. Tran,Huu M. Tran,Elad Noor,Jasmine L. Gallaher,Jacob B. Bale,Yasuo Yoshikuni,Yasuo Yoshikuni,Michael H. Gelb,Jay D. Keasling,Barry L. Stoddard,Mary E. Lidstrom,David Baker +19 more
TL;DR: A computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule is described, demonstrating how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway.
Journal ArticleDOI
Computational Design of an α-Gliadin Peptidase
Sydney Gordon,Elizabeth Joy Stanley,Sarah Jane Wolf,Angus Toland,Sean J. Wu,Daniel Hadidi,Jeremy H. Mills,David Baker,Ingrid Swanson Pultz,Justin B. Siegel +9 more
TL;DR: Through identification of a natural enzyme with the pre-existing qualities relevant to an ultimate goal and redefinition of its substrate specificity using computational modeling, this work was able to generate an enzyme with potential as a therapeutic for celiac disease.