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.