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The RosettaDock server for local protein–protein docking

The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein–protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting...

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Detalles Bibliográficos
Autores principales: Lyskov, Sergey, Gray, Jeffrey J.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447798/
https://www.ncbi.nlm.nih.gov/pubmed/18442991
http://dx.doi.org/10.1093/nar/gkn216
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author Lyskov, Sergey
Gray, Jeffrey J.
author_facet Lyskov, Sergey
Gray, Jeffrey J.
author_sort Lyskov, Sergey
collection PubMed
description The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein–protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.
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spelling pubmed-24477982008-07-09 The RosettaDock server for local protein–protein docking Lyskov, Sergey Gray, Jeffrey J. Nucleic Acids Res Articles The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein–protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge. Oxford University Press 2008-07-01 2008-04-28 /pmc/articles/PMC2447798/ /pubmed/18442991 http://dx.doi.org/10.1093/nar/gkn216 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Lyskov, Sergey
Gray, Jeffrey J.
The RosettaDock server for local protein–protein docking
title The RosettaDock server for local protein–protein docking
title_full The RosettaDock server for local protein–protein docking
title_fullStr The RosettaDock server for local protein–protein docking
title_full_unstemmed The RosettaDock server for local protein–protein docking
title_short The RosettaDock server for local protein–protein docking
title_sort rosettadock server for local protein–protein docking
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447798/
https://www.ncbi.nlm.nih.gov/pubmed/18442991
http://dx.doi.org/10.1093/nar/gkn216
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