Abstract
Analysis of the global properties of protein sequences, rather than single-site or local properties, has been shown to lead to new understanding of folding and function. Here we describe the use of software which can describe sequences numerically in an orthonormal fashion, Fourier-analyze those sequences, and verify the statistical significance of the resulting Fourier coefficients. The resulting parameters can be used to study problems involving sequences from a unique perspective.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Rackovsky S (1998) Hidden sequence periodicities and protein architecture. Proc Natl Acad Sci USA 95:8580–8584
Rackovsky S (2006) Characterization of architecture signals in proteins. J Phys Chem B 110:18771–18778
Kidera A, Konishi Y, Oka M et al (1985) Statistical analysis of the physical properties of the 20 naturally occurring amino acids. J Prot Chem 4:23–55
Kidera A, Konishi Y, Ooi T et al (1985) Relation between sequence similarity and structural similarity in proteins: role of important properties of amino acids. J Prot Chem 4:265–297
Rackovsky S (2009) Sequence physical properties encode the global organization of protein structure space. Proc Natl Acad Sci USA 106:14345–14348
Rackovsky S (2010) Global characteristics of protein sequences and their implications. Proc Natl Acad Sci USA 107:8623–8626
Rackovsky S (2011) Spectral analysis of a protein conformational switch. Phys Rev Lett 106:248101
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media New York
About this protocol
Cite this protocol
Rackovsky, S. (2012). Beyond Supersecondary Structure: The Global Properties of Protein Sequences. In: Kister, A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 932. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-065-6_7
Download citation
DOI: https://doi.org/10.1007/978-1-62703-065-6_7
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-064-9
Online ISBN: 978-1-62703-065-6
eBook Packages: Springer Protocols