proteinko 3.0.0

Proteinko is used for modeling distributions of psysicochemical properties of proteins

Proteinko

Proteinko is used for modeling distributions of psysicochemical properties of proteins.

• About
• Installation
• Usage

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About

Protein is a sequence of amino acid residues, each characterized by a set of physical and chemical properties. By modeling properties of individual amino acid residues, mapping them to single vector representing a protein sequence and summing the overlapping portions of modeled amino acid residues, proteinko yields a distribution of physicochemical properties of protein sequence.

Proteinko has built-in schemas for following properties, although it allows adding custom schemas for any real or theoretical property of amino acid residues:

• Hydropathy
• Donor hydrogen bonds
• Acceptor hydrogen bonds
• Isoelectric point
• Van der Waals volume

Installation

pip install proteinko

Usage

To start we are going to import class called Proteinko from proteinko package and initialize the instance of the class.

from proteinko import Proteinko

prt = Proteinko()

To list available physicochemical properties we can use the built-in method get_schemas(). This should produce the following output.

schemas = prt.get_schemas()
print(schemas)

>>> ['hydropathy', 'acceptors', 'donors', 'pI', 'volume']

This looks fine, but let's add one of our own schemas. We are going to use Kyte-Doolittle hydropathy schema which is stored in a CSV file located in local resources/ directory.

prt.add_schema(
    'resources/kyte_doolittle.csv', 
    amino_col=0, 
    value_col=1, 
    key='kd', 
    header=1
)

To clarify what we did here, we passed the path to the csv file, specified the columns which contain amino acid residues and corresponding values, provided a key under which the data will be stored and let the parser know the file has 1 header row. Now if we print schemas we should see following output.

print(prt.get_schemas())

>>> ['hydropathy', 'acceptors', 'donors', 'pI', 'volume', 'kd']

Finally, in order to get a distribution of Kyte-Doolittle hydropathy across protein sequence, let's first define our protein sequence and than call the function get_dist() passing the sequence and schema as function arguments.

sequence = 'ILKEPVHGV'
dist = prt.get_dist(sequence, 'kd')

If we plot our modeled distribution it should look something like this.