Protein folding · Monte Carlo

Gō Model: Protein Folding Free Energy

Gō Model: Protein Folding Free Energy
fig. Gō Model: Protein Folding Free Energy

The notebook · live in your browser, code and all

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The notebook runs on its own once it loads, so give it about 10 seconds while Python starts up in your browser, and the simulations begin animating. Move the sliders and everything recomputes live. The code is shown alongside the output so you can read exactly how it works; the full editable source is linked below.

A simplified, off-lattice Go model of a small protein, folded with Monte Carlo. The payoff is the free energy landscape as a function of the fraction of native contacts: the folded basin, the unfolded one, the barrier between them, and the temperature where folding tips over. It is the coarse-grained, statistical-mechanics picture of folding, and it connects directly to the spectroscopy I did in the biophysics lab.

Code & resources

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