Overview

Binding Curve Viewer is a set of tools to visualize and simulate the equilibrium and kinetics of binding reactions with 1:1 stoichiometry and no cooperativity for experiment planning and validation. To use the tools online, please visit the website. Source code can be found at GitHub.

Requirements

1. Visualization Tools (Python Environment)

To generate the visualization tools of Binding Curve Viewer, the following dependencies are required:

1. Python >= 3.7.6

2. Bokeh >= 3.4.0

3. Numpy >= 1.26.0

2. Interactive Simulation Tools (R Environment)

To run the interactive simulation components, ensure you have installed:

1. R and R Packages: shiny(>= 1.13.0), bslib, ggplot2, minpack.lm, KSgeneral

Usage

Visit the website to use the online tools. Or download the source code from GitHub Page and run binding_curve_viewer_v2.py to get all the visualization tools of Binding Curve Viewer. To use the interactive simulation components, run the corresponding scripts in R environment.

How to Cite

Du, Y. 2024. Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein–Ligand Binding and Competitive Binding. J. Chem. Inf. Model. 64(10):4180-4192. [Free Full Text from Publisher] [PubMed]

License of the code

MIT License

Copyright (c) 2026 Yu Du

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

License of the webpages

CC BY 4.0