Methods in Enzymology, pages 545-574
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Andrew Leaver-Fay
1
,
Michael D. Tyka
2
,
Steven M. Lewis
1
,
Oliwia Lange
2
,
James Thompson
2
,
Ron Jacak
1
,
Kristian W. Kaufman
3
,
P Douglas Renfrew
4
,
Colin A. Smith
5
,
William Sheffler
2
,
Ian Davis
6
,
Seth Cooper
2
,
Adrien Treuille
7
,
Daniel J Mandell
5
,
FLORIAN RICHTER
2
,
Yih-En Andrew Ban
8
,
Jacob E Corn
2
,
David D. Kim
2
,
Sergey Lyskov
9
,
Monica Berrondo
10
,
Stuart Mentzer
11
,
Zoran Popović
6
,
James J Havranek
12
,
John Karanicolas
13
,
Purvesh Khatri
14
,
Jens Meiler
3
,
Tanja Kortemme
5
,
Jeffrey J. Gray
15
,
Brian Kuhlman
1
,
David Baker
2
,
Philip T. Bradley
16
1
Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, USA
|
6
GrassRoots Biotechnology
7
CARNEGIE MELLON UNIVERSITY
|
8
Arzeda Corporation
10
Rosetta Design Group LLC
11
Objexx Engineering
12
Washington University St. Louis
|
13
University Of Kansas
|
Publication type: Book Chapter
Publication date: 2011-01-01
Journal:
Methods in Enzymology
Quartile SCImago
— Quartile WOS
—
Impact factor: —
ISSN: 00766879, 15577988
PubMed ID:
21187238
Abstract
We have recently completed a full re-architecturing of the ROSETTA molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy-to-use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as ROSETTA3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.
Top-30
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Journal of the American Chemical Society
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eLife
17 publications, 1.11%
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International Journal of Molecular Sciences
16 publications, 1.04%
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16 publications, 1.04%
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Computational and Structural Biotechnology Journal
15 publications, 0.98%
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Journal of Computational Chemistry
15 publications, 0.98%
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Journal of Chemical Theory and Computation
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Nucleic Acids Research
14 publications, 0.91%
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Current Opinion in Structural Biology
13 publications, 0.85%
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Nature
12 publications, 0.78%
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BMC Bioinformatics
12 publications, 0.78%
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Journal of Physical Chemistry B
12 publications, 0.78%
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11 publications, 0.72%
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Methods in Enzymology
10 publications, 0.65%
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Protein Engineering, Design and Selection
10 publications, 0.65%
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Citations by publishers
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250
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Elsevier
248 publications, 16.12%
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Springer Nature
241 publications, 15.67%
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Cold Spring Harbor Laboratory
191 publications, 12.42%
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Wiley
150 publications, 9.75%
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American Chemical Society (ACS)
137 publications, 8.91%
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Public Library of Science (PLoS)
82 publications, 5.33%
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Oxford University Press
74 publications, 4.81%
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Proceedings of the National Academy of Sciences (PNAS)
45 publications, 2.93%
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Multidisciplinary Digital Publishing Institute (MDPI)
44 publications, 2.86%
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American Society for Biochemistry and Molecular Biology
35 publications, 2.28%
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American Association for the Advancement of Science (AAAS)
27 publications, 1.76%
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Frontiers Media S.A.
24 publications, 1.56%
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American Society for Microbiology
18 publications, 1.17%
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Royal Society of Chemistry (RSC)
17 publications, 1.11%
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eLife Sciences Publications
17 publications, 1.11%
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Association for Computing Machinery (ACM)
17 publications, 1.11%
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International Union of Crystallography (IUCr)
15 publications, 0.98%
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Taylor & Francis
12 publications, 0.78%
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IEEE
10 publications, 0.65%
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Biophysical Society
9 publications, 0.59%
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American Institute of Physics (AIP)
8 publications, 0.52%
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Portland Press
8 publications, 0.52%
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Mary Ann Liebert
5 publications, 0.33%
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Cambridge University Press
5 publications, 0.33%
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PeerJ
4 publications, 0.26%
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World Scientific
4 publications, 0.26%
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Annual Reviews
4 publications, 0.26%
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American Society for Pharmacology and Experimental Therapeutics
3 publications, 0.2%
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The Royal Society
3 publications, 0.2%
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50
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- We do not take into account publications without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Leaver-Fay A. et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. // Methods in Enzymology. 2011. pp. 545-574.
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Leaver-Fay A., Tyka M. D., Lewis S. M., Lange O., Thompson J., Jacak R., Kaufman K. W., Renfrew P. D., Smith C. A., Sheffler W., Davis I., Cooper S., Treuille A., Mandell D. J., RICHTER F., Ban Y. A., Fleishman S. J., Corn J. E., Kim D. D., Lyskov S., Berrondo M., Mentzer S., Popović Z., Havranek J. J., Karanicolas J., Khatri P., Meiler J., Kortemme T., Gray J. J., Kuhlman B., Baker D., Bradley P. T. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. // Methods in Enzymology. 2011. pp. 545-574.
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TY - GENERIC
DO - 10.1016/B978-0-12-381270-4.00019-6
UR - https://doi.org/10.1016/B978-0-12-381270-4.00019-6
TI - ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
T2 - Methods in Enzymology
AU - Leaver-Fay, Andrew
AU - Tyka, Michael D.
AU - Lewis, Steven M.
AU - Lange, Oliwia
AU - Thompson, James
AU - Jacak, Ron
AU - Kaufman, Kristian W.
AU - Renfrew, P Douglas
AU - Smith, Colin A.
AU - Sheffler, William
AU - Davis, Ian
AU - Cooper, Seth
AU - Treuille, Adrien
AU - Mandell, Daniel J
AU - RICHTER, FLORIAN
AU - Ban, Yih-En Andrew
AU - Fleishman, Sarel J
AU - Corn, Jacob E
AU - Kim, David D.
AU - Lyskov, Sergey
AU - Berrondo, Monica
AU - Mentzer, Stuart
AU - Popović, Zoran
AU - Havranek, James J
AU - Karanicolas, John
AU - Khatri, Purvesh
AU - Meiler, Jens
AU - Kortemme, Tanja
AU - Gray, Jeffrey J.
AU - Kuhlman, Brian
AU - Baker, David
AU - Bradley, Philip T.
PY - 2011
DA - 2011/01/01 00:00:00
PB - Elsevier
SP - 545-574
PMID - 21187238
SN - 0076-6879
SN - 1557-7988
ER -
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@incollection{2011_Leaver-Fay,
author = {Andrew Leaver-Fay and Michael D. Tyka and Steven M. Lewis and Oliwia Lange and James Thompson and Ron Jacak and Kristian W. Kaufman and P Douglas Renfrew and Colin A. Smith and William Sheffler and Ian Davis and Seth Cooper and Adrien Treuille and Daniel J Mandell and FLORIAN RICHTER and Yih-En Andrew Ban and Sarel J Fleishman and Jacob E Corn and David D. Kim and Sergey Lyskov and Monica Berrondo and Stuart Mentzer and Zoran Popović and James J Havranek and John Karanicolas and Purvesh Khatri and Jens Meiler and Tanja Kortemme and Jeffrey J. Gray and Brian Kuhlman and David Baker and Philip T. Bradley},
title = {ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.},
publisher = {Elsevier},
year = {2011},
pages = {545--574},
month = {jan}
}