claffinity 1.0.1

A tool for investigating the impact of labelled ligand affinity in competition experiments.

competition-label-affinity

A tool for investigating the impact of labelled ligand affinity in competition experiments. Code accompanies the paper "Optimum ligand affinity for competition-based primary screens" by Shave et. al.

Requirements

Code 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)
• mpmath (1.1.0)

Program definitions

01_plot_protein_needed_vs_ligand_kd.py

• Plot ligand pKD vs conc protein needed to achieve desired (default = .7) fraction ligand bound.

01_plot_singal_vs_ligand_kd_fixed_inhibitor.py

• Plot ligand pKD vs fraction ligand bound

01_simulate_competition_experiment.py

• Simultate a simple single point from a competition experiment.

02_inhibitorKD_vs_fractionBound.py

• Simulate inhibitor pKD vs fraction ligand bound

02_inhibitorKD_vs_fractionBound_animation.py

• Generate animation of inhibitor pKD vs fraction ligand bound over a range of ligand pKDs in the animation.

02_inhibitorKD_vs_fractionBound_interactive.py

• Interactive plot of inhibitor pKD vs fraction ligand bound over a range of changable ligand pKDs.

02_ligandKD_vs_fractionBound.py

• Plot ligand pKD vs fraction ligand bound in the presence of a fixed concentration of inhibitor with fixed KD.

02_ligandKD_vs_fractionBound_animation.py

• Generate animation for ligand pKD vs fraction ligand bound, varying ligand KD over time.

02_ligandKD_vs_fractionBound_interactive.py

• Interactive plot of ligand pKD vs fraction ligand bound, varying inhibitor KD.

03_ligandKD_vs_fractionBoundAsPercentSignalReduction.py

• Plot ligand pKD vs percent signal reduction in the presence of a fixed concentration of inhibitor with fixed KD.

04_missed_inhibitors.py

• Simulate real world example whereby inhibitors would be missed in a primary screen using high affinity ligands.

05_KDPL_vs_FLB_VaryingTargetFLB.py

• Plot pKD of ligand vs fraction ligand bound, varying the target fraction ligand bound from the default 0.7.

06_KDPL_vs_FLB_VaryingL0.py

• Plot pKD of ligand vs fraction ligand bound, varying the amount of ligand present.

07_KDPL_vs_FLB_VaryingI0.py

• Plot pKD of ligand vs fraction ligand bound, varying the amount of inhibitor present.

08_HuangPlot.py

• Reproduce the Huang plot (Huang, X., Fluorescence polarization competition assay: the range of resolvable inhibitor potency is limited by the affinity of the fluorescent ligand. Journal of biomolecular screening 2003, 8 (1), 34-38.)