helloannekim / zlotnick-drug-sim

Zlotnick drugs!

zlotnick-drug-sim

Why: Understand the behavior of viral capsid assembly in the absence and presence of varying drug concentrations.

Scope:

1. Reproduce viral capsid assembly model from "A Theoretical Model Successfully Identifies Features of Hepatitis B Virus Capsid" by Zlotnick et al. Model will use ODE's with KroneckerBio Systems Biology Modeling in MATLAB for the assembly of capsid monomers to form a final dodecahedron capsid.
2. Extend Zlotnick model to include varying concentrations of drugged monomers.

Status: Unfinished. Added all helper code. TODO: update drugging code"

Zlotnick1999.m fits figure 1B from Zlotnick 1999 paper, but doesn't account for the slow nucleation steps of dimer and trimer reactions. Mysterious.

Zlotnick1999_KLm reveals that following prescribed slower nucleation at dimerization but faster elongation later does not actually reproduce Zlotnick figure 1B.

Zlotnick1999_Concentration_Dependence.m redeems the model by reasonably reproducing figure 4D, while following the model of a slower nucleation and faster elongation.