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Welcome to Receptors

Receptor Modeling

Overview
States and transitions
Ligand binding
Thermodynamic constraints
Equilibrium formalism
Tools and Examples - Part 1

Receptor Dimers

Overview
Reduced Graph Powers
Tools and Examples - Part 2
Enumerating allosteric parameters

Fitting Allosteric Parameters

Overview
Fitting allosteric parameters
Example lmfit
example-minimize-linear-regression.ipynb
Minimize receptor model pade

Nonequilibrium steady states

Markov chain receptor models
Non-equilibrium steady states
Hill’s diagrammatic method
Tools and Examples - Part 3

Cycle Fluxes

Overview
Cycle fluxes in receptor models
Reduced Graph Powers
Derived Markov chains
Double Derived Markov chain w/ contexts
Double Derived Markov chain w/ contexts
Further Reading

Wang algebras

Wang algebra
Wang algebra - undirected graph
Wang algebra - directed graph

Appendix

Example graphs
Example Reduced Graph Powers
BFS Spanning Tree
docstring test
My struggle with docstrings
Plotting hypercube graphs
practicing python
Receptor Tools
Receptor Tools - Cycle Fluxes and Derived Markov chain

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By Greg Conradi Smith

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