-
Notifications
You must be signed in to change notification settings - Fork 34
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Regarding input and distance matrix padding. #27
Comments
Interesting comments.:
The codebase is from a year and a half ago so I don't have everything in my mind now. If you could clarify what you're referring to, I think I would be able to explain more. Thanks for the interest in the project! |
Hi!! Thanks for the quick reply!
Another question is: you did used Alpha Carbons as distance targets, right? You wrote that you applied the Model to ProteinNet, but it doesn't stores Beta Carbon coordinates, only N, Ca, C (CBeta being the "root" of side chain). I'm asking this because I've been trying to fetch the Beta Carbon coordinates from ProteinNet ids and been getting several issues regarding sequence/structure matching between PDB and ProteiNet. Thanks a lot again for the answer. have you been doing any other works in protein structure prediction? And, nice paper on E-Swish. |
Cool!
Thanks for the E-swish comment, i did it during my last high school year! Also, what do you think about my comment in the other thread? |
Hi!
Wonderful work here, and wonderful code aswell.
I have a few questions regarding your model and some of your input preparation steps.
1- Why do you implemented padding as a new class and not as a mask, by multiplaying every add layer by this binary mask in order to avoid backprop of these regions?
2- Why did you created a different embbeding for the distances, and not only the threshold function?
The text was updated successfully, but these errors were encountered: