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.
- 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
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
To install this module, run the following commands:
perl Makefile.PL
make
make test
make install
After installing, you can find documentation for this module with the perldoc command.
perldoc Bio::Protease
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.