S
Sagar D. Khare
Researcher at Rutgers University
Publications - 87
Citations - 5589
Sagar D. Khare is an academic researcher from Rutgers University. The author has contributed to research in topics: Medicine & Chemistry. The author has an hindex of 29, co-authored 70 publications receiving 4469 citations. Previous affiliations of Sagar D. Khare include University of North Carolina at Chapel Hill & University of Saskatchewan.
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Journal ArticleDOI
Quantitative reactivity profiling predicts functional cysteines in proteomes
Eranthie Weerapana,Chu Wang,Gabriel M. Simon,Florian Richter,Sagar D. Khare,Myles B. D. Dillon,Daniel A. Bachovchin,Kerri A. Mowen,David Baker,Benjamin F. Cravatt +9 more
TL;DR: It is demonstrated that quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs.
Journal ArticleDOI
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
Sarel J. Fleishman,Andrew Leaver-Fay,Jacob E. Corn,Eva-Maria Strauch,Sagar D. Khare,Nobuyasu Koga,Justin Ashworth,Paul Murphy,Florian Richter,Gordon Lemmon,Jens Meiler,David Baker +11 more
TL;DR: RosettaScripts protocols for the stabilization of proteins, the generation of computationally constrained libraries for experimental selection of higher-affinity binding proteins, loop remodeling, small-molecule ligand docking, design of ligand-binding proteins, and specificity redesign in DNA- binding proteins are illustrated.
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
Computational design of ligand-binding proteins with high affinity and selectivity.
Christine E. Tinberg,Sagar D. Khare,Jiayi Dou,Lindsey Doyle,Jorgen Nelson,Alberto Schena,Wojciech Jankowski,Charalampos G. Kalodimos,Kai Johnsson,Barry L. Stoddard,David Baker +10 more
TL;DR: A general computational method for designing pre-organized and shape complementary small-molecule-binding sites is described, and used to generate protein binders to the steroid digoxigenin (DIG).
Journal ArticleDOI
De novo enzyme design using Rosetta3.
TL;DR: Here, it is demonstrated how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction.