Mathematical process for protein folding

[Hopper_18]

TL;DR Summary

Trying to determine if there is a mathematical process for protein folding that can be done without a computer to create a new protein that’s function would be a combination of multiple real life protein.

Hello, I am currently working on an idea for a possible future masters or PhD in cellular biology, however my idea is currently just a passion project. For it to work, I would need to learn how to predict and make a specific protein to do a specific function, in this instance I need to use it to inhibit the transcription of certain DNA region by finding to different CDK and cycling.

I have been some research into this but have found no website or otherwise study describing how one could go about doing this, without substantial expertise and a super computer. Even then it was comparing it to other already recognized proteins in which the function would be similar.

I was wondering if anyone could explain how one might create a protein to do a specific function in which the desired function would be a combination of multiple proteins in real life? Also is there a way to determine this protein folding mathematically or otherwise without a computer, or is purely computer based?

Thank you for any information that you can provide.

 

[Tom.G]

From what little I know of the subject, it seems to be a combinatorial problem.
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Yup, I asked Google:
https://www.google.com/search?&q=why+is+protein+folding+hard

This being the first response:
...the protein interacts with surrounding water when folding. So you have more like 30k atoms to simulate

Unless your IQ is in the 5 or 6 digit range and have an eidetic memory, get access to a LARGE computer.

Have Fun!
Tom

 

[pinball1970]

From what little I know of the subject, it seems to be a combinatorial problem.
.
.
.
Yup, I asked Google:
https://www.google.com/search?&q=why+is+protein+folding+hard

This being the first response:
...the protein interacts with surrounding water when folding. So you have more like 30k atoms to simulate

Unless your IQ is in the 5 or 6 digit range and have an eidetic memory, get access to a LARGE computer.

Have Fun!
Tom

Some threads this year on the subject including the Alpha 2 program. I will dig out.

 

[Hornbein]

TL;DR Summary: Trying to determine if there is a mathematical process for protein folding that can be done without a computer to create a new protein that’s function would be a combination of multiple real life protein.

Hello, I am currently working on an idea for a possible future masters or PhD in cellular biology, however my idea is currently just a passion project. For it to work, I would need to learn how to predict and make a specific protein to do a specific function, in this instance I need to use it to inhibit the transcription of certain DNA region by finding to different CDK and cycling. I have been some research into this but have found no website or otherwise study describing how one could go about doing this, without substantial expertise and a super computer. Even then it was comparing it to other already recognized proteins in which the function would be similar. I was wondering if anyone could explain how one might create a protein to do a specific function in which the desired function would be a combination of multiple proteins in real life? Also is there a way to determine this protein folding mathematically or otherwise without a computer, or is purely computer based? Thank you for any information that you can provide.

I believe that protein folding is a very hard problem. The hope is that it can be solved by quantum computers, or perhaps artificial intelligence will be good enough.

 

[pinball1970]

I believe that protein folding is a very hard problem. The hope is that it can be solved by quantum computers, or perhaps artificial intelligence will be good enough.

Some links in this thread.

Thread 'AI-Powered AlphaFold 2: Revolutionizing Protein Folding' https://www.physicsforums.com/threa...ld-2-revolutionizing-protein-folding.1002982/

 

[pinball1970]

This is a study to measure the presence of the stages of folding using NMR.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.132.048402