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 calculating the iep of a protein, based on bioperl’s approach. It can be installed as a gem. It is currently been refactored to fit as a bioruby plugin.

Supported PKA sets

Support for the following Pka sets is available

dta_select
emboss
rodwell
wikipedia
sillero

You can also create a custom Pka set as shown in the example

Installation

gem install 'bio'
gem install 'isoelectric_point'

Usage

require 'bio'
require 'isoelectric_point'

protein_seq = Bio::Sequence::AA.new("KKGFTCGELA")

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

#calculate the ph using dtaselect pka set and round off to 3 decimal places

isoelectric_point = protein_seq.calculate_iep('dtaselect', 3)   #=>8.219

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

Authors

George Githinji -- KEMRI-Wellcome Trust Research program ([email protected])
Pascal Betz     -- Simplificator GmbH