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Bio::Protease

Digest your protein substrates with customizable specificity

This module models the hydrolitic behaviour of a proteolytic enzyme. Its main purpose is to predict the outcome of hydrolitic cleavage of a peptidic substrate.

The enzyme specificity is currently modeled for 33 enzymes/reagents. This models are somewhat simplistic as they are largely regex-based, and do not take into account subtleties such as kinetic/temperature effects, accessible solvent area, secondary or tertiary structure elements. However, the module is flexible enough to allow the inclusion of any of these effects via user-defined regexes or by consuming the ProteaseI role.

Currently implemented specificities:

  • Alcalase
  • Arg-c Proteinase
  • asp-n Endopeptidase
  • asp-n Endopeptidase Glu
  • BNPS Skatole
  • Caspase 1
  • Caspase 2
  • Caspase 3
  • Caspase 4
  • Caspase 5
  • Caspase 6
  • Caspase 7
  • Caspase 8
  • Caspase 9
  • Caspase 10
  • Chymotrypsin high specificity
  • Chymotrypsin low specificity
  • Clostripain
  • CNBr
  • Enterokinase
  • Factor Xa
  • Formic Acid
  • Glutamyl Endopeptidase
  • GranzymeB
  • Hydroxylamine
  • Iodosobenzoic acid
  • Lys C
  • Lys N
  • NTCB
  • Pepsin pH 1.3
  • Pepsin
  • Proline Endopeptidase
  • Proteinase K
  • Staphylococcal Peptidase I
  • Thermolysin
  • Thrombin
  • Trypsin
  • HCl

Support for custom specificities

You can customize your protease's specificity either consuming the Bio::ProteaseI role, or using a custom regex in the specificity attribute. The underlying model allows for up to 8 residues surrounding the siscile bond (P4-P1, P1'-P4'):

.----..----.----..----. .-----.-----.-----.-----.
| A  || M  | Q  || R  |*|  N  |  L  |  A  |  W  |
|----||----|----||----|^|-----|-----|-----|-----|
| P4 || P3 | P2 || P1 ||| P1' | P2' | P3' | P4' |
'----''----'----''----'|'-----'-----'-----'-----'
                  cleavage site

Installation

To install this module, run the following commands:

perl Makefile.PL
make
make test
make install

Support and Documentation

After installing, you can find documentation for this module with the perldoc command.

perldoc Bio::Protease

Copyright and Licence

Copyright (C) 2010 Bruno Vecchi

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

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