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An effective all-atom potential for proteins

Irbäck, Anders LU ; Mitternacht, Simon LU and Mohanty, Sandipan (2009) In Food Biophysics 2(1). p.2-2
Abstract

We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49-67-residue systems with high statistical accuracy, using only modest computational resources by... (More)

We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49-67-residue systems with high statistical accuracy, using only modest computational resources by today's standards.PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc.

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publication status
published
in
Food Biophysics
volume
2
issue
1
pages
2 - 2
publisher
Springer
ISSN
1557-1866
DOI
10.1186/1757-5036-2-2
language
English
LU publication?
yes
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ee6950b3-55b0-4e93-bf2f-bd52246ec717
date added to LUP
2016-08-16 18:30:39
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2016-10-21 07:42:49
@article{ee6950b3-55b0-4e93-bf2f-bd52246ec717,
  abstract     = {<p>We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49-67-residue systems with high statistical accuracy, using only modest computational resources by today's standards.PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc.</p>},
  author       = {Irbäck, Anders and Mitternacht, Simon and Mohanty, Sandipan},
  issn         = {1557-1866},
  language     = {eng},
  number       = {1},
  pages        = {2--2},
  publisher    = {Springer},
  series       = {Food Biophysics},
  title        = {An effective all-atom potential for proteins},
  url          = {http://dx.doi.org/10.1186/1757-5036-2-2},
  volume       = {2},
  year         = {2009},
}