D
Daisuke Kuroda
Researcher at University of Tokyo
Publications - 76
Citations - 3055
Daisuke Kuroda is an academic researcher from University of Tokyo. The author has contributed to research in topics: Medicine & Chemistry. The author has an hindex of 21, co-authored 63 publications receiving 2153 citations. Previous affiliations of Daisuke Kuroda include Showa University & Osaka University.
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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
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).
Sergey Lyskov,Fang-Chieh Chou,Shane Ó Conchúir,Bryan S. Der,Kevin Drew,Daisuke Kuroda,Jianqing Xu,Brian D. Weitzner,P. Douglas Renfrew,Parin Sripakdeevong,Benjamin Borgo,James J. Havranek,Brian Kuhlman,Tanja Kortemme,Richard Bonneau,Richard Bonneau,Jeffrey J. Gray,Rhiju Das +17 more
TL;DR: This paper describes the ROSIE server infrastructure, a step-by-step ‘serverification’ protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams.
Journal ArticleDOI
Three-dimensional hole drilling of silica glass from the rear surface with femtosecond laser pulses.
Yan Li,Kazuyoshi Itoh,Wataru Watanabe,Kazuhiro Yamada,Daisuke Kuroda,Junji Nishii,Yongyuan Jiang +6 more
TL;DR: Three-dimensional channels can be micromachined inside transparent materials by use of this method, as it is demonstrated by drilling a square-wave-shaped hole inside silica glass.
Journal ArticleDOI
Computer-aided antibody design.
TL;DR: This review summarizes recent progresses in the field of computer-aided antibody development mainly focusing on antibody modeling, which is divided essentially into two parts: modeling the antigen-binding site, also called the complementarity determining regions (CDRs), and predicting the relative orientations of the variable heavy and light chains.
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.