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Modeling the structure of helical assemblies with experimental constraints in Rosetta

André, Ingemar LU (2018) In Methods in Molecular Biology 1764. p.475-489
Abstract

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass... (More)

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

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author
organization
publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
subject
keywords
Fibers, Fibrils, Helical assemblies, Helical symmetry, Rosetta, Structure determination, Structure prediction
in
Methods in Molecular Biology
volume
1764
pages
15 pages
publisher
Humana Press
external identifiers
  • scopus:85044834668
ISSN
1064-3745
DOI
10.1007/978-1-4939-7759-8_30
language
English
LU publication?
yes
id
c59f9054-4c89-4d09-936d-5982c9d78f86
date added to LUP
2018-04-16 14:07:48
date last changed
2018-04-17 03:00:02
@inbook{c59f9054-4c89-4d09-936d-5982c9d78f86,
  abstract     = {<p>Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.</p>},
  author       = {André, Ingemar},
  issn         = {1064-3745},
  keyword      = {Fibers,Fibrils,Helical assemblies,Helical symmetry,Rosetta,Structure determination,Structure prediction},
  language     = {eng},
  month        = {01},
  pages        = {475--489},
  publisher    = {Humana Press},
  series       = {Methods in Molecular Biology},
  title        = {Modeling the structure of helical assemblies with experimental constraints in Rosetta},
  url          = {http://dx.doi.org/10.1007/978-1-4939-7759-8_30},
  volume       = {1764},
  year         = {2018},
}