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Binary assignments of amino acids from pattern conservation

Irbäck, A LU and Potthast, F LU (1997) In Protein Engineering 10(9). p.7-1013
Abstract

We have developed a simple optimization procedure for assigning binary values to amino acids. The binary values are determined by a maximization of the degree of pattern conservation in groups of closely related protein sequences. The maximization is carried out at fixed composition. For compositions approximately corresponding to an equipartition of the residues, the optimal encoding is found to be strongly correlated with hydrophobicity. The stability of the procedure is demonstrated. Our calculations are based upon sequences in the SWISS-PROT database.

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author
organization
publishing date
type
Contribution to journal
publication status
published
keywords
Amino Acids, Databases, Factual, Fourier Analysis, Models, Chemical, Peptide Mapping, Protein Folding, Proteins
in
Protein Engineering
volume
10
issue
9
pages
5 pages
publisher
Oxford University Press
external identifiers
  • Scopus:2642657329
ISSN
0269-2139
DOI
doi: 10.1093/protein/10.9.1013
language
English
LU publication?
yes
id
444792c4-94c8-49f5-8c8a-52e1f8baf556
date added to LUP
2016-08-17 16:29:58
date last changed
2016-10-13 05:12:28
@misc{444792c4-94c8-49f5-8c8a-52e1f8baf556,
  abstract     = {<p>We have developed a simple optimization procedure for assigning binary values to amino acids. The binary values are determined by a maximization of the degree of pattern conservation in groups of closely related protein sequences. The maximization is carried out at fixed composition. For compositions approximately corresponding to an equipartition of the residues, the optimal encoding is found to be strongly correlated with hydrophobicity. The stability of the procedure is demonstrated. Our calculations are based upon sequences in the SWISS-PROT database.</p>},
  author       = {Irbäck, A and Potthast, F},
  issn         = {0269-2139},
  keyword      = {Amino Acids,Databases, Factual,Fourier Analysis,Models, Chemical,Peptide Mapping,Protein Folding,Proteins},
  language     = {eng},
  number       = {9},
  pages        = {7--1013},
  publisher    = {ARRAY(0xb5ffcd0)},
  series       = {Protein Engineering},
  title        = {Binary assignments of amino acids from pattern conservation},
  url          = {http://dx.doi.org/doi: 10.1093/protein/10.9.1013 },
  volume       = {10},
  year         = {1997},
}