P
P. Douglas Renfrew
Researcher at New York University
Publications - 38
Citations - 4448
P. Douglas Renfrew is an academic researcher from New York University. The author has contributed to research in topics: Chemistry & Medicine. The author has an hindex of 16, co-authored 29 publications receiving 2929 citations. Previous affiliations of P. Douglas Renfrew include Courant Institute of Mathematical Sciences & New York University Abu Dhabi.
Papers
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Book ChapterDOI
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Andrew Leaver-Fay,Michael D. Tyka,Steven M. Lewis,Oliver F. Lange,James Thompson,Ron Jacak,Kristian W. Kaufman,P. Douglas Renfrew,Colin A. Smith,William Sheffler,Ian W. Davis,Seth Cooper,Adrien Treuille,Daniel J. Mandell,Florian Richter,Yih-En Andrew Ban,Sarel J. Fleishman,Jacob E. Corn,David E. Kim,Sergey Lyskov,Monica Berrondo,Stuart Mentzer,Zoran Popović,James J. Havranek,John Karanicolas,Rhiju Das,Jens Meiler,Tanja Kortemme,Jeffrey J. Gray,Brian Kuhlman,David Baker,Philip Bradley +31 more
TL;DR: This chapter describes the requirements for the ROSETTA molecular modeling program's new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.
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.
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.
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.