pICalculax

Isoelectric point (pI) predictor for chemically modified peptides and proteins.

For handling conversion of PLN to condensed molformat, Proteax desktop is needed.

A modification database for import is found in the mods_db directory

For handling condensed molfile formats, RDKit needs to be patched. Patch can be found in the rdkit_patch directory.

Example usage can be found in the file Example_usage.py

Example Usage interactive session

fasta = 'ICECREAM'

from pICalculax import find_pKas, pI
from rdkit import Chem

mol = Chem.MolFromFASTA(fasta)

#find pKa values and charge class
pkalist, charge = find_pKas(mol)
#Calculate pI
pIpred = pI(pkalist, charge)

print pIpred

The peptides can be loaded from a SDfile

#!/usr/bin/python
""" Example usage of the pICalculax for pI prediction of unmodified and modified peptides """

from __future__ import print_function
from pICalculax import find_pKas, pI
from rdkit import Chem
from rdkit.Chem import Draw


#Load a protein from SD file in condensed format
sdsup = Chem.SDMolSupplier('Datasets/example_mols.sdf')

def predict_show(mol):
	#Get list of identified pKa values and charge
	pkalist, charge = find_pKas(mol)
	#Predict the pI from the identified pKa values
	piPred = pI(pkalist, charge)
	#Report and Visualize
	print("Predicted pI:%0.2F"%piPred)
	Draw.ShowMol(mol, legend = "Predicted pI:%0.2F"%piPred)
	Draw.tkRoot.update()
	txt = raw_input('Press <ENTER> to continue')

# An unmodified peptide
mol = sdsup[0]
predict_show(mol)

# A peptide with a modification
mol = sdsup[1]
predict_show(mol)

With Proteax Desktop protein line notation of modified peptides can be converted to a RDKit mol object and the pI predicted

from proteax_desktop import *
prtx = ProteaxDesktop()

pln = 'H-GHANY[Gla]A-OH'

mol = Chem.MolFromMolBlock(prtx.as_molfile(pln,'expansion-mode=condensed'))

#find pKa values and charge class
pkalist, charge = find_pKas(mol)
#Calculate pI
pIpred = pI(pkalist, charge)

print pIpred

Command line usage

$ python pICalculax.py -h
usage: pICalculax.py [-h] [--fasta FASTA [FASTA ...]] [--pln PLN [PLN ...]]

Predict isoeletric point pI of peptides and modified peptides

optional arguments:
  -h, --help            show this help message and exit
  --fasta FASTA [FASTA ...]
                        Predict fasta sequence
  --pln PLN [PLN ...]   Predict PLN sequence (Requires Proteax Desktop)

#Fasta
$ python pICalculax.py --fasta ICECREAM FATCAT
4.14 	ICECREAM
5.02 	FATCAT

#Protein line notation (Requires Proteax Desktop)
$ python pICalculax.py --pln H-GHANYEA-OH H-GHANY[Gla]A-OH
5.41 	H-GHANYEA-OH
4.77 	H-GHANY[Gla]A-OH

References

Please cite

http://pubs.acs.org/doi/10.1021/acs.jcim.7b00030

@article{doi:10.1021/acs.jcim.7b00030,
author = {Bjerrum, Esben J. and Jensen, Jan H. and Tolborg, Jakob L.},
title = {pICalculax: Improved Prediction of Isoelectric Point for Modified Peptides},
journal = {Journal of Chemical Information and Modeling},
volume = {57},
number = {8},
pages = {1723-1727},
year = {2017},
doi = {10.1021/acs.jcim.7b00030},
    note ={PMID: 28671456},

URL = { 
        http://dx.doi.org/10.1021/acs.jcim.7b00030
    
},
eprint = { 
        http://dx.doi.org/10.1021/acs.jcim.7b00030
    
}

}

Commercial Support

Commercial support is available from

www.wildcardconsulting.dk

or

www.biochemfusion.com