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A simplified amino acid potential for use in structure predictions of proteins

Wallqvist, A. and Ullner, M. LU (1994) In Proteins: Structure, Function, and Bioinformatics 18(3). p.267-280
Abstract

A simplified description and a corresponding force field for polypeptides is introduced. Each amino acid residue is reduced to one interaction site, representing the backbone, and one or two side chain sites depending on its size and complexity. Site–site interactions are parameterized after a hydrophobicity criterium. The treatment of backbone sites is in addition designed to reproduce typical polypeptide hydrogen bonding patterns, as well as yielding conformations in accord with the allowed ϕ and ψ angles through an effective angle potential. There are no explicit charges in the model. The derived energy functions, which are based on thermodynamic data and sterical consideration of allowed backbone conformations, correspond to the... (More)

A simplified description and a corresponding force field for polypeptides is introduced. Each amino acid residue is reduced to one interaction site, representing the backbone, and one or two side chain sites depending on its size and complexity. Site–site interactions are parameterized after a hydrophobicity criterium. The treatment of backbone sites is in addition designed to reproduce typical polypeptide hydrogen bonding patterns, as well as yielding conformations in accord with the allowed ϕ and ψ angles through an effective angle potential. There are no explicit charges in the model. The derived energy functions, which are based on thermodynamic data and sterical consideration of allowed backbone conformations, correspond to the introduction of an effective potential. The model is tested on two small proteins, avian pancreatic polypeptide and a parathyroid hormone‐related protein, by simulating folding from an initially extended state using Monte Carlo methods. The reduced amino acid description is able to satisfactorily reproduce the experimentally determined native structures.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
avian pancreatic polypeptide, effective backbone interactions, folding, hydrophobicity, Monte Carlo, parathyroid hormone‐related protein
in
Proteins: Structure, Function, and Bioinformatics
volume
18
issue
3
pages
14 pages
publisher
John Wiley & Sons
external identifiers
  • scopus:0028347939
ISSN
0887-3585
DOI
10.1002/prot.340180308
language
English
LU publication?
yes
id
8a77cafd-fd42-4600-8848-b5abed0b6ab8
date added to LUP
2018-03-29 10:48:18
date last changed
2018-05-29 09:36:00
@article{8a77cafd-fd42-4600-8848-b5abed0b6ab8,
  abstract     = {<p>A simplified description and a corresponding force field for polypeptides is introduced. Each amino acid residue is reduced to one interaction site, representing the backbone, and one or two side chain sites depending on its size and complexity. Site–site interactions are parameterized after a hydrophobicity criterium. The treatment of backbone sites is in addition designed to reproduce typical polypeptide hydrogen bonding patterns, as well as yielding conformations in accord with the allowed ϕ and ψ angles through an effective angle potential. There are no explicit charges in the model. The derived energy functions, which are based on thermodynamic data and sterical consideration of allowed backbone conformations, correspond to the introduction of an effective potential. The model is tested on two small proteins, avian pancreatic polypeptide and a parathyroid hormone‐related protein, by simulating folding from an initially extended state using Monte Carlo methods. The reduced amino acid description is able to satisfactorily reproduce the experimentally determined native structures. <br/></p>},
  author       = {Wallqvist, A. and Ullner, M.},
  issn         = {0887-3585},
  keyword      = {avian pancreatic polypeptide,effective backbone interactions,folding,hydrophobicity,Monte Carlo,parathyroid hormone‐related protein},
  language     = {eng},
  number       = {3},
  pages        = {267--280},
  publisher    = {John Wiley & Sons},
  series       = {Proteins: Structure, Function, and Bioinformatics},
  title        = {A simplified amino acid potential for use in structure predictions of proteins},
  url          = {http://dx.doi.org/10.1002/prot.340180308},
  volume       = {18},
  year         = {1994},
}