J
Jeliazko R. Jeliazkov
Researcher at Johns Hopkins University
Publications - 36
Citations - 2446
Jeliazko R. Jeliazkov is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Epitope & Paratope. The author has an hindex of 11, co-authored 33 publications receiving 1214 citations. Previous affiliations of Jeliazko R. Jeliazkov include University of Zurich & University of Illinois at Urbana–Champaign.
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Journal ArticleDOI
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.
Rebecca F. Alford,Andrew Leaver-Fay,Jeliazko R. Jeliazkov,Matthew J. O’Meara,Frank DiMaio,Hahnbeom Park,Maxim V. Shapovalov,P. Douglas Renfrew,Vikram Khipple Mulligan,Kalli Kappel,Jason W. Labonte,Michael S. Pacella,Richard Bonneau,Philip Bradley,Roland L. Dunbrack,Rhiju Das,David Baker,Brian Kuhlman,Tanja Kortemme,Jeffrey J. Gray +19 more
TL;DR: This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15), and explains how to use Rosetta energies to identify and analyze the features of biomolecular models.
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.
Posted ContentDOI
The Rosetta all-atom energy function for macromolecular modeling and design
Rebecca F. Alford,Andrew Leaver-Fay,Jeliazko R. Jeliazkov,Matthew J. O’Meara,Frank DiMaio,Hahnbeom Park,Maxim V. Shapovalov,P. Douglas Renfrew,Vikram Khipple Mulligan,Kalli Kappel,Jason W. Labonte,Michael S. Pacella,Richard Bonneau,Philip Bradley,Roland L. Dunbrack,Rhiju Das,David Baker,Brian Kuhlman,Tanja Kortemme,Jeffrey J. Gray +19 more
TL;DR: The mathematical models and physical concepts that underlie the latest Rosetta energy function, beta_nov15, and the latest advances in the energy function that extend capabilities from soluble proteins to also include membrane proteins, peptides containing non-canonical amino acids, carbohydrates, nucleic acids, and other macromolecules are discussed.
Journal ArticleDOI
Modeling and docking of antibody structures with Rosetta
Brian D. Weitzner,Jeliazko R. Jeliazkov,Sergey Lyskov,Nicholas A. Marze,Daisuke Kuroda,Daisuke Kuroda,Rahel Frick,Rahel Frick,Jared Adolf-Bryfogle,Jared Adolf-Bryfogle,Naireeta Biswas,Roland L. Dunbrack,Jeffrey J. Gray +12 more
TL;DR: Rosetta-based computational protocols for predicting the 3D structure of an antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock) are described and can be run fully automated via the ROSIE web server or manually on a computer with user control of individual steps.
Journal ArticleDOI
Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors
Jay H. Kalin,Jay H. Kalin,Muzhou Wu,Andrea V. Gómez,Yun Song,Jayanta Kumar Das,Dawn Hayward,Nkosi Adejola,Mingxuan Wu,Mingxuan Wu,Izabela P. Panova,Hye Jin Chung,Edward Kim,Holly J. Roberts,Justin M. Roberts,Polina Prusevich,Jeliazko R. Jeliazkov,Shourya S. Roy Burman,Louise Fairall,Charles P. Milano,Abdulkerim Eroglu,Charlotte M. Proby,Albena T. Dinkova-Kostova,Albena T. Dinkova-Kostova,Wayne W. Hancock,Jeffrey J. Gray,Jeffrey J. Gray,James E. Bradner,Sergio Valente,Antonello Mai,Nicole M. Anders,Michelle A. Rudek,Yong Hu,Byungwoo Ryu,John W.R. Schwabe,Andrea Mattevi,Rhoda M. Alani,Philip A. Cole,Philip A. Cole +38 more
TL;DR: A bifunctional small molecule inhibitor that simultaneously targets the deacetylase (HDAC1) and demethylase (LSD1) activities of the CoREST complex is reported, highlighting the promise of a new class of two-pronged hybrid agents that may show preferential targeting of particular epigenetic regulatory complexes and offer unique therapeutic opportunities.