pyProtein

pyProtein does basic calculations on polypeptides/proteins/enzymes. Methods are contained in class protein. Is intended to be included into scripts for automated calculations.

Currently only calculations for compounds with amino acid residues (proteins/ enzymes/polypeptides) are supported (so no synthetic polymers). As an input, the protein composition as amino acid abundance or amino acid sequence must be given.

The package contains functions for charge calculations of proteins:

• The calculations are done with the Henderson-Hasselbalch equation, assuming that the individual amino acid residues do not show interactions which alter the pK_a values to a relevant extent. As such, the calculations are done similar to e.g. the "ExPASy Compute pI/Mw tool" or the "Prot pi | Protein Tool".
• Calculates the charge states of proteins at a given pH value.
• Calculates the charge curve of proteins, i.e. the protein charge in a given pH value interval.
• Calculates the isoelectric point (IEP) of proteins.
• The charges can be given as total charge, separated into postive/negative charges, or as charges carried by the individual amino acids.
• Currently contains four different pK_a data tables for IEP and charge calculations (Bjellqvist, IPC, IPC2, EMBOSS). It is relatively straight-forward to implement other pK_a tables is necessary.

The package can calculate some other protein properties:

• Nitrogen content
• Molar mass
• Mean residue molar mass
• Elemental composition

The package can handle chemical protein modifications:

• Can take modifications into account for calculated protein properties, such as IEP, molar mass, or nitrogen content.
• Currently implemented modifications are methacryl modifications of amino/hydroxy groups and aminoethyl modifications of carboxylic acid groups.
• N- and C-terminal amino and carboxylic acid groups are also treated as modifications. I they should be taken into account for the calculations, they need to be included explicitly.
• Other modifications must be listed with their characteristics in the DataFrame chain_modifications (see amino_acid_properties.py). Implemenation is rather easy.

For imformation on how to use it:

• See docstrings.
• Or look at how the tests are done in the tests folder.

Requirements

Requirements are listed in the requirements.txt file.

Installation

Download repository and run:

pip install -e .

pyProtein is also part of PyPI, so install with:

pip install pyProtein

However, the newest version can always be found here.