Binary assignments of amino acids from pattern conservation
(1997) In Protein Engineering 10(9). p.1013-1017- 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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https://lup.lub.lu.se/record/444792c4-94c8-49f5-8c8a-52e1f8baf556
- author
- Irbäck, A LU and Potthast, F LU
- organization
- publishing date
- 1997-09
- 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
- pmid:9464565
- ISSN
- 0269-2139
- 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
- 2024-01-04 11:00:42
@article{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}}, keywords = {{Amino Acids; Databases, Factual; Fourier Analysis; Models, Chemical; Peptide Mapping; Protein Folding; Proteins}}, language = {{eng}}, number = {{9}}, pages = {{1013--1017}}, publisher = {{Oxford University Press}}, series = {{Protein Engineering}}, title = {{Binary assignments of amino acids from pattern conservation}}, url = {{http://dx.doi.org/10.1093/protein/10.9.1013}}, doi = {{10.1093/protein/10.9.1013}}, volume = {{10}}, year = {{1997}}, }