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Size dependent complexity of sequences in protein families

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  • J. Li
  • J. Wang
  • W. Wang

Abstract

The size dependent complexity of protein sequences in various families in the FSSP database is characterized by sequence entropy, sequence similarity and sequence identity. As the average length L f of sequences in the family increases, an increasing trend of the sequence entropy and a decreasing trend of the sequence similarity and sequence identity are found. As L f increases beyond 250, a saturation of the sequence entropy, the sequence similarity and the sequence identity is observed. Such a saturated behavior of complexity is attributed to the saturation of the probability P g of global (long-range) interactions in protein structures when L f >250. It is also found that the alphabet size of residue types describing the sequence diversity depends on the value of L f , and becomes saturated at 12. Copyright EDP Sciences/Società Italiana di Fisica/Springer-Verlag 2005

Suggested Citation

  • J. Li & J. Wang & W. Wang, 2005. "Size dependent complexity of sequences in protein families," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 47(3), pages 431-436, October.
    • Handle: RePEc:spr:eurphb:v:47:y:2005:i:3:p:431-436
    DOI: 10.1140/epjb/e2005-00333-x
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