Documentation of Binding Curve Viewer

Understanding the thermodynamics and kinetics of the protein-ligand interaction is essential for biologists and pharmacologists. Binding Curve Viewer is a tool to visualize the equilibrium and kinetics of binding reaction 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.

User Guide

• Overview
  • Requirements
  • Usage
  • How to Cite
  • License of the code
  • License of the webpages
• Functions
  • Determination of Dissociation Constant
  • Kinetics of Association and Dissociation
  • Iso-affinity Plot
  • Competitive Binding of Association
  • Competitive Binding of Dissociation
  • Simulation of High-Throughput Screening
• Scripts
  • association_curve_fitting.py
  • ic50.py
  • ki_app_calc.py & ki_app_calc_small_insert.py
  • association_curve_fitting_SI_1.py
  • association_curve_fitting_SI_2.py
  • ki_app_calc_mpmath.py
  • pl_kd_relationship_perc.py
  • detailed_kd_ki_pl.py
  • cubic_equation_rounding_error.py
• Appendix 1
  • Solutions of differential equations and equilibrium concentrations
    • Kinetics of the second-order binding process
    • Thermodynamics of the second-order binding process
    • Kinetics of the pseudo-first-order binding process
    • Thermodynamics of the pseudo-first-order binding process
    • Kinetics of the dissociation process
• Appendix 2
  • The calculation of the K_i and apparent K_i
    • Calculation of the apparent K_i by the Cheng-Prusoff equation
    • Calculation of the apparent K_i by the Lin-Riggs equation
    • Calculation of the K_i by the Wang’s group equation
• Reference