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 32 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 subclassing.

### Currently implemented specificities:

* 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 subclassing
Bio::ProteaseI, 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) 2009 **Bruno Vecchi**

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