search

PabloCatalan / toylife

Code to run toyLIFE, a multi-level model of the genotype-phenotype map
5 stars 0 forks source link

HP Model Implementation #2

Open cgoliver opened 2 years ago

cgoliver commented 2 years ago

Hello,

Just wondering if you could kindly point me to the implementation of the HP model you used for folding the proteins. From what I can tell these were pre-computed, but I'm not 100% sure.

Thanks!

Carlos

PabloCatalan commented 2 years ago

Hey Carlos,

Thanks for writing!

The details of the HP model we implemented can be read in the Supplementary Material of one of our papers: https://pablocatalan.github.io/papers/catalan2018_toyLIFE_complexity_SM.pdf

(pages 2 to 4 of the PDF)

But yes, it's precomputed. It's easy to find all the self-avoiding walks (SAWs) that cover a 4x4 lattice, and then remove symmetries. We found 38 different Saws. Once we had them, we forced every sequence to fold into every SAW and then selected the SAW that minimized the free energy of the protein. We then discarded the folding and recorded only the perimeter and energy, and named each unique combination of perimeter plus folding energy a protein.

Hope this helps Pablo

El mar., 14 jun. 2022 15:06, Carlos Oliver @.***> escribió:

Hello,

Just wondering if you could kindly point me to the implementation of the HP model you used for folding the proteins. From what I can tell these were pre-computed, but I'm not 100% sure.

Thanks!

Carlos

— Reply to this email directly, view it on GitHub https://github.com/PabloCatalan/toylife/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC3IJ7BMBGVRYU24ZYEEAADVPB7W7ANCNFSM5YXUUS2A . You are receiving this because you are subscribed to this thread.Message ID: @.***>

cgoliver commented 2 years ago

Thank you for this, and the explanation that helps a lot :)

cgoliver commented 2 years ago

Did you explicitly enumerate all self-avoiding walks on the 4x4 lattice or were these taken from another result?

PabloCatalan commented 2 years ago

Yes, they were enumerated. I didn't do that part, Clemente F Arias did it using Mathematica. But it shouldn't be hard to do it by brute force.

El mié, 15 jun 2022 a las 14:47, Carlos Oliver @.***>) escribió:

Did you explicitly enumerate all self-avoiding walks on the 4x4 lattice or were these taken from another result?

— Reply to this email directly, view it on GitHub https://github.com/PabloCatalan/toylife/issues/2#issuecomment-1156428403, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC3IJ7EJNE3QCEAJKNYQUBLVPHGFLANCNFSM5YXUUS2A . You are receiving this because you commented.Message ID: @.***>

-- Pablo Catalán Profesor Ayudante Doctor Universidad Carlos III de Madrid https://pablocatalan.github.io Twitter: @the100footpole