Open cgoliver opened 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
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Thank you for this, and the explanation that helps a lot :)
Did you explicitly enumerate all self-avoiding walks on the 4x4 lattice or were these taken from another result?
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?
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-- Pablo Catalán Profesor Ayudante Doctor Universidad Carlos III de Madrid https://pablocatalan.github.io Twitter: @the100footpole
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