Hello, I am studying proteomics right now, and I have a question for you FAH experts:
Wikipedia declares:
(see wikipedia article "Protein_tertiary_structure")
<<No currently existing algorithm is yet able to consistently predict a proteins' tertiary or quaternary structure given only its primary structure; learning how to accurately predict the tertiary and quaternary structure of any protein given only its amino acid sequence and the pertinent cellular conditions would be a monumental achievement.>>
I understand that sometimes folding takes a lot of time because every time the protein flaps randomly against itself there is only a certain probability of it attaching to itself in the correct final shape.
However if this was the only problem, the only problem would be false negatives, i.e., no folding obtained.
I got the impression, by reading from elsewhere, that the real primary problem in ab-initio folding is the false-positive thing: a protein that folds in-silico in an incorrect folding. So you think it's correct but it's not. And that's why you need actual confirmation by X-ray cristallography.
Ok then, this is the question: why the in-silico folds are not validated with quantum mechanics simulations? Refer to
(See wikipedia article "Molecular_dynamics")
I understand that the whole folding simulation is way too long to be performed fully in quantum mechanics, however only a few tens of picoseconds of quantum mechanics simulation would be needed in order to validate the fold you have obtained with classical MD. You need to re-simulate only the, say, 50ps in which the protein flaps against itself and attaches to itself. If it really attaches, ok, if not, it was a false positive and the folding simulation has to be discarded/repeated...
Why isn't this done?
Thanks for your insight
Why misfolds?
Moderators: Site Moderators, FAHC Science Team
Return to “The Science of FAH -- questions/answers”
Jump to
- Announcements
- ↳ Announcements - Folding Consortium
- ↳ Announcements - Forum related
- New Donors
- ↳ New Donors start here
- Current Software
- ↳ V8.3.xx Open Beta
- ↳ V8.1.xx Open Beta
- ↳ V7.6.x Public Release Windows/Linux/MacOS X
- ↳ V7.5.1 Public Release Windows/Linux/MacOS X [deprecated]
- ↳ Software for ARM hardware
- ↳ Q&A about unsupported distros of Linux
- ↳ New GPUs (whitelist)
- ↳ Android client from Sony (deprecated)
- GPU drivers
- ↳ Problems with NVidia drivers
- ↳ Windows 10 + NVidia
- ↳ Problems with AMD/ATI drivers
- ↳ Intel iGP Drivers
- Stats and server issues
- ↳ Issues with a specific server
- ↳ Issues with a specific WU
- ↳ CPU Projects - released FAHCores _a7 & _a8 (a4 retired)
- ↳ GPU Projects and FahCores
- ↳ Issues with this forum
- ↳ CPU Projects - beta FAHCores (Currently _a8)
- General Discussions
- ↳ Discussions of General-FAH topics
- ↳ How can we help FAH grow
- ↳ The Science of FAH -- questions/answers
- ↳ Scientific discussions (Non-FAH)
- ↳ FAH Hardware
- ↳ In memoriam
- 3rd party software
- ↳ 3rd party contributed software