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A knowledge‐basedscale for amino acidmembrane propensity Marco PuntaAmos Maritan2002 год

A knowledge‐based scale for amino acid membrane propensity
статья из журнала

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Аннотация: Abstract In this article, a membrane‐propensity scale for amino acids is derived using only two ingredients: (i) a set of transmembrane helices segments from membrane protein crystal structures and (ii) the request that each component of the set has a free energy lower than that of a typical soluble protein sequence of the same length. Although the most widely used hydropathy scales satisfy this request, we use an optimization procedure that allows for extraction of an optimal scale, which correlates equally well with those scales. We show that, if the choice of the sequence database is accurate, significant knowledge‐based scales, which are robust with respect to changes in the learning set, can be easily derived. The obtained scales can be used for transmembrane helices prediction. The predictive power of one of these scales is tested on membrane proteins, soluble proteins, and signal peptides databases, finding that its performances is comparable with those of the hydropathy scales. Proteins 2003;50:114–121. © 2002 Wiley‐Liss, Inc.
Год издания: 2002
Авторы: Marco Punta, Amos Maritan
Издательство: Wiley
Источник: Proteins Structure Function and Bioinformatics
Ключевые слова: Machine Learning in Bioinformatics, RNA and protein synthesis mechanisms, Protein Structure and Dynamics
Другие ссылки: Proteins Structure Function and Bioinformatics (HTML)
PubMed (HTML)