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Bio-Tools-Solubility-Wilkinson-0.093360
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/ Bio::Tools::Solubility::Wilkinson

NAME

Bio::Tools::Solubility::Wilkinson - Calculate the probability of a protein to be soluble using the Wilkinson-Harrison model

VERSION

version 0.093360

SYNOPSIS

use Bio::Tools::Solubility::Wilkinson;

my $seq = 'MMAEELLVIKP...';

my $s = solubility($seq);

DESCRIPTION

This module implements a simple method for the prediction of protein solubility, as described by Wilkinson, D.L. and Harrison [1] and modified by Davis [2]. It only takes the primary sequence of the protein as a parameter, and returns the calculated probability that the protein will be expressed in soluble form in E. Coli.

It uses aminoacid composition to compute the two main parameters found to have strong correlation with solubility: charge average and turn forming residue fraction. For a detailed description of the formula used, check the article by Harrison [3] in the References section.

METHODS

solubility

Returns the probability of the sequence $seq being soluble. $seq should be a correct and validated protein sequence written in one-letter aminoacid code. Any whitespace (spaces, newlines, tabs, etc) will be ignored.

my $probability = solubility($seq);

This function is exported by default.

Customize your imports

If you'd like to rename the only imported subroutine for some reason, you can do:

use Bio::Tools::Solubility::Wilkinson
    solubility => { -as => 'solubility_wilkinson' };

use Some::Other::Solubility::Module 'solubility_foo';

my $p1 = solubility_wilkinson($seq);
my $p2 = solubility_foo($seq);

This (and other goodies) are possible thanks to Sub::Exporter, which is worth checking out.

References

  • [1] Wilkinson, D.L. and Harrison, R.G. (1991). Predicting the solubility of recombinant proteins in Escherichia coli BioTechnology 9, 443-448.

  • [2] Gregory D. Davis, Claude Elisee, Denton M. Newham, Roger G. Harrison (1999). New fusion protein systems designed to give soluble expression in Escherichia coli. Biotechnology and Bioengineering Volume 65 Issue 4, Pages 382 - 388

  • [3] R.G. Harrison. 2000. Expression of soluble heterologous proteins via fusion with NusA protein. inNovations. 11:4-7. http://www.biotech.ou.edu/innovations.pdf

AUTHOR

Bruno Vecchi <vecchi.b gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2009 by Bruno Vecchi.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.