A simplified amino acid potential for use in structure predictions of proteins
(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.
(Less)
- author
- Wallqvist, A. and Ullner, M. LU
- organization
- publishing date
- 1994
- 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 Inc.
- external identifiers
-
- scopus:0028347939
- pmid:8202468
- 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
- 2024-01-14 17:46:26
@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}},
keywords = {{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 Inc.}},
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}},
doi = {{10.1002/prot.340180308}},
volume = {{18}},
year = {{1994}},
}