pybindingcurve 1.0.0

Protein ligand binding simulation in Python

PyBindingCurve

PyBindingCurve is a Python package for simulation, plotting and fitting of experimental parameters to protein-ligand binding systems at equilibrium. In simple terms, the most basic functionality allows simulation of a two species binding to each other as a function of their concentrations and the dissociation constant (K_D) between the two species. A number of systems are built in and can be solved using direct analytical, kinetic, or Langrange multiplier based techniques. User-defined custom systems can also be specified using a simple syntax.

Installation

PyBindingCurve may be installed from source present in the GitHub repository https://github.com/stevenshave/pybindingcurve via git pull, or from the Python Package Index (https://pypi.org/project/pybindingcurve/) using the command :

pip install pybindingcurve

Requirements

PyBindingCurve was developed using python 3.7.1 but should work with any Python version 3.6 or greater. The following packages are also required

• Matplotlib (2.x)
• Numpy (1.15.x)
• lm_fit (1.0.0)
• mpmath (1.1.0)

Licence

MIT License

Usage

A tutorial and API documentation can be found here

A quickstart example for simulation of protein-ligand binding is as follows:

import numpy as np
import pybindingcurve as pbc
my_system = pbc.BindingCurve("1:1")
system_parameters = {"p": np.linspace(0, 20), "l": 10, "kdpl": 1}
my_system.add_curve(system_parameters)
my_system.show_plot()

Authors

PyBindingCurve was written by Steven Shave

Please get in contact for custom solutions, integration to existing workflows and training.