Advanced

Identification of amino acid sequences with good folding properties in an off-lattice model

Irbäck, Anders LU ; Peterson, Carsten LU and Potthast, Frank LU (1997) In Physical Review E 55(1 SUPPL. B). p.860-867
Abstract

Folding properties of a two-dimensional toy protein model containing only two amino acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding... (More)

Folding properties of a two-dimensional toy protein model containing only two amino acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences. © 1997 The American Physical Society.

(Less)
Please use this url to cite or link to this publication:
author
publishing date
type
Contribution to journal
publication status
published
in
Physical Review E
volume
55
issue
1 SUPPL. B
pages
8 pages
publisher
American Physical Society
external identifiers
  • Scopus:18844424885
ISSN
1063-651X
DOI
10.1103/PhysRevE.55.860
language
English
LU publication?
no
id
934e7dc7-0ba3-4c49-991f-900f8ad21a65
date added to LUP
2016-08-17 17:58:14
date last changed
2016-09-13 15:41:32
@misc{934e7dc7-0ba3-4c49-991f-900f8ad21a65,
  abstract     = {<p>Folding properties of a two-dimensional toy protein model containing only two amino acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences. © 1997 The American Physical Society.</p>},
  author       = {Irbäck, Anders and Peterson, Carsten and Potthast, Frank},
  issn         = {1063-651X},
  language     = {eng},
  number       = {1 SUPPL. B},
  pages        = {860--867},
  publisher    = {ARRAY(0xb10dde0)},
  series       = {Physical Review E},
  title        = {Identification of amino acid sequences with good folding properties in an off-lattice model},
  url          = {http://dx.doi.org/10.1103/PhysRevE.55.860},
  volume       = {55},
  year         = {1997},
}