Build Status

bio-isoelectric_point

The isoelectric point (pI), sometimes abbreviated to iep, is the pH at which a particular molecule or surface carries no net electrical charge.

This library is a Ruby implementation for estimating the isoelectric point of a protein.

The following Pka sets are supported

* dtaselect
* emboss
* rodwell
* wikipedia
* sillero
*Custom Pka sets are also supported

Installation

gem install bio-isoelectric_point

Uninstallation

gem uninstall bio-isoelectric_point

Usage

require 'bio-isoelectric_point'

#create  a protein sequence amino acid object
protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")

#what is the protein charge at ph 14?
charge = protein_seq.charge_at(14)     #=>-2.999795857467562

#calculate the pH using dtaselect pka set and round off to 3 decimal places
isoelectric_point = protein_seq.isoelectric_point('dtaselect', 3) #=>8.219

#calculate the iep ph with a custom set
custom_pka_set = { "N_TERMINUS" => 8.1,
                   "C_TERMINUS" => 3.15,
                            "K" => 10.1,
                            "R" => 12.1,
                            "H" => 6.4,
                            "D" => 4.34,
                            "E" => 4.33,
                            "C" => 8.33,
                            "Y" => 9.5
                 }
iep_ph = protein_seq.isoelectric_point(custom_pka_set, 3) #=> 8.193

Contributing to bio-isoelectric_point

Copyright ©2011 George Githinji. See LICENSE.txt for more details.