Numerical Methods for the Life Scientist (eBook)

Introduction
Classical enzyme kinetics
Classical dose-response curves and the Hill coefficient
Classical association and dissociation kinetics and exponential fits
Numerical methods
Preparing the computer
Installation of Octave for different platforms
Installation of Linux
Running the provided programs
Data input and output
Binding equilibria
Analytical and numerical solution for equilibrium binding to one site
Equilibrium binding to two or more sites.
Equilibrium binding to two or more conformational states
Equilibrium binding for oxygen to hemoglobin (MWC model)
Equilibrium binding of more than one ligand (e.g. agonist and inhibitor)
Enzyme kinetics as coupled equilibria
Enzyme kinetics with competitive or noncompetitive inhibitors
Dose-response curves for receptor agonists and enzyme inhibitors
Binding kinetics
Ligand binding kinetics of first and second order
Numerical solutions of differential equations
Calculation of true enzyme kinetics
Dissociation by dilution and dissociation by competition (“chase”)
States and sites
Least squares fit to experimental data
The function lsqcurvefit
Comparing correct binding curves with Hill equations
Comparing real binding kinetics with current multi-exponential fits
Fitting experimental data
Causes for errors
Multi-parameter fits
Correlation of parameters
Selecting a model and minimizing the number of parameters
Degrees of freedom
Global Fits
Significance of parameters in multi-parameter fits
Comparing the two different approaches
Model independent versus model calculations
Global fit versus single fits
Make ends meet: Try to analyze reported data with new methods
Designing experiments for complete analysis
Appendix
Description of program files
Sample data
Comparing MATLAB and Octave code