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Interpretable Numerical Descriptors of Amino Acid Space
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2009 (English)In: Journal of Computational Biology, ISSN 1066-5277, E-ISSN 1557-8666, Vol. 16, no 5, 703-723 p.Article in journal (Refereed) Published
Abstract [en]

Informative numerical representations of amino acid residues are essential for successful in silico modeling or establishing the structure-activity relationships of proteins. A straightforward approach is adopted here for representing more than 500 amino acid indices from the AAindex database by a set of uncorrelated scales, satisfying the VARIMAX criterion. Different measures are considered in order to demonstrate the improved interpretability of the current scales as compared to previously published ones. Performance is also addressed in a classification problem of G-protein coupled receptors, and is found to be similar or higher than the performance achieved by six other scale sets. Finally, a unique correspondence between numerical indices and mutation matrices is derived and discussed in light of the evolutionary conservation of amino acid properties. Conclusions from this study highlight the discord between ease of interpretation of amino acid scales and their relevance to protein structure conservation, as well as general considerations for designing custom scale sets.

Place, publisher, year, edition, pages
2009. Vol. 16, no 5, 703-723 p.
Keyword [en]
algorithms, linear algebra, sequence analysis
National Category
Biochemistry and Molecular Biology Natural Sciences
Identifiers
URN: urn:nbn:se:su:diva-60044DOI: 10.1089/cmb.2008.0173ISI: 000266508800005OAI: oai:DiVA.org:su-60044DiVA: diva2:433787
Note
authorCount :1Available from: 2011-08-11 Created: 2011-08-08 Last updated: 2017-12-08Bibliographically approved

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