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Macromolecular modeling and design in Rosetta: recent methods and frameworks

by Kortemme, Tanja , Frenz, Brandon , Norn, Christoffer , Malmström, Lars , Pilla, Kala Bharath , Sevy, Alexander M. , Bonneau, Richard , Khar, Karen R. , Huber, Thomas , Lubin, Joseph H. , Marcu, Orly , Ó’Conchúir, Shane , Maguire, Jack , Khare, Sagar D. , Rubenstein, Aliza , Lewis, Steven M. , Coventry, Brian , Baker, David , Geniesse, Caleb , Horowitz, Scott , Labonte, Jason W. , Smith, Shannon , Zimmerman, Lior , Marze, Nicholas A. , Pavlovicz, Ryan E. , Nerli, Santrupti , Goldschmidt, Lukasz , Siegel, Justin B. , Renfrew, P. Douglas , Khatib, Firas , Szegedy, Maria , Leman, Julia Koehler , Kuenze, Georg , Ovchinnikov, Sergey , Pethe, Manasi , Ollikainen, Noah , Das, Rhiju , Gray, Jeffrey J. , Dunbrack, Roland , Lapidoth, Gideon , Khramushin, Alisa , Alford, Rebecca F. , Bender, Brian J. , Khakzad, Hamed , Kleffner, Robert , Pan, Xingjie , Song, Yifan , Thyme, Summer B. , Bradley, Phil , Kappel, Kalli , Guffy, Sharon , Meiler, Jens , Ford, Alexander S. , Schief, William , Bystroff, Chris , Jacobs, Tim M. , Burman, Shourya S. Roy , Barth, Patrick , Koepnick, Brian , Dsilva, Lorna , Pacella, Michael S. , Correia, Bruno E. , Schueler-Furman, Ora , Teets, Frank D. , Silva, Dan

in 631/114/2411 / 631/114/469 / 631/114/794 / 631/57/2266 / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Computer programs / Design / Docking / Interfaces / Interoperability / Laboratories / Life Sciences / Macromolecular Substances - chemistry / Macromolecules / Modelling / Models, Molecular / Molecular Docking Simulation / Molecules / Peptidomimetics - chemistry / Perspective / Protein Conformation / Proteins - chemistry / Proteomics / Software / User interfaces

2020

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Macromolecular modeling and design in Rosetta: recent methods and frameworks

2020

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2020

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Journal Article

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Kortemme, Tanja,

Frenz, Brandon,

Norn, Christoffer,

Malmström, Lars,

Pilla, Kala Bharath,

Sevy, Alexander M.,

Bonneau, Richard,

Khar, Karen R.,

Huber, Thomas,

Lubin, Joseph H.,

Marcu, Orly,

Ó’Conchúir, Shane,

Maguire, Jack,

Khare, Sagar D.,

Rubenstein, Aliza,

Lewis, Steven M.,

Coventry, Brian,

Baker, David,

Geniesse, Caleb,

Horowitz, Scott,

Labonte, Jason W.,

Smith, Shannon,

Zimmerman, Lior,

Marze, Nicholas A.,

Pavlovicz, Ryan E.,

Nerli, Santrupti,

Goldschmidt, Lukasz,

Siegel, Justin B.,

Renfrew, P. Douglas,

Khatib, Firas,

Szegedy, Maria,

Leman, Julia Koehler,

Kuenze, Georg,

Ovchinnikov, Sergey,

Pethe, Manasi,

Ollikainen, Noah,

Das, Rhiju,

Gray, Jeffrey J.,

Dunbrack, Roland,

Lapidoth, Gideon,

Khramushin, Alisa,

Alford, Rebecca F.,

Bender, Brian J.,

Khakzad, Hamed,

Kleffner, Robert,

Pan, Xingjie,

Song, Yifan,

Thyme, Summer B.,

Bradley, Phil,

Kappel, Kalli,

Guffy, Sharon,

Meiler, Jens,

Ford, Alexander S.,

Schief, William,

Bystroff, Chris,

Jacobs, Tim M.,

Burman, Shourya S. Roy,

Barth, Patrick,

Koepnick, Brian,

Dsilva, Lorna,

Pacella, Michael S.,

Correia, Bruno E.,

Schueler-Furman, Ora,

Teets, Frank D.,

Silva, Dan

2020

Overview

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org . This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.

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Publisher

Nature Publishing Group US,Nature Publishing Group

Subject

/ Biological Microscopy

/ Biological Techniques