I am looking for existing quantum algorithms for the prediction of the tertiary structure of proteins.
Do you know of any? Joachim's links made me realize that I forgot to specify the type of algorithms I am focusing on, namely, ab initio quantum algorithms.
This question is closed. Thank you all.
Dear Renata,
What do you mean by out there? (Note that the 'out there'ness is a philosophical question).Thank you for the answer.
@Marc Carvallo
I just meant any that I do not know of. Nothing philosophical about it. The part is now deleted as it appears to detract readers from the gist of my question.
Dear Renata,
(i) Do you mean that 'out there' is deleted? Why? Because it appears to detract readers from the gist of your question?
(ii) Don't forget that philosophy is the foundation of any science.
Thanks in advance for your answer. Marc.
Dear Renata,
Pretty good and interesting conversation between you and Dr. Marc Carvallo! However, could you please explain whether you want to apply quantum algorithm on an external quantum circuit to solve the protein folding problem or you want to see protein itself as a quantum computer to compute it’s own folding pathway. In the first case I would like to comment, what is the use of fast computation when we don’t have any physical principle to guide molecular motion. For example, in case of energy minimization principle we have a rough energy landscape. In the second case, as long as we don’t have any identified entangled states how could we hope to apply quantum algorithm?
Dear Mohammad,
Yes, it is not always possible to find a common frequency.
Regarding your question, it is the first case. I would like to write an algorithm for the PSP problem that could be run on a quantum circuit. Ideally it would be good to see what others have done so far, hence my question. There appears not to be many research papers on the topic.
The fact that protein dynamics is not fully understood yet hasn't deterred researchers from developing classical algorithms based on our limited understanding of what drives the folding process. They hold a biannual assessment (CASP) of newest methods in this field. So there seems to be some progress here. Admittedly, this series of trials and errors is not an ideal approach. But before we can be offered better access to the quantum realm, guessing and logical reasoning will be parts of the "scientific" method I guess.
If Levinthal's paradox is honored the first approach might not help for the PSP problem, I guess...
That is why the crux of a quantum algorithm lies in exploiting the underlying structure of a problem, finding which might not be easy, admittedly, and then using the interference effect to eliminate unwanted results and amplify the preferred ones.
I think that at this stage when designing algorithms one should probably not be so much bothered by the time aspect of the folding process but rather try to figure out the mechanism leading to the structure.
No quantum algorithm, but possibly interesting:
https://deepmind.com/blog/alphafold/
https://www.theguardian.com/science/2018/dec/02/google-deepminds-ai-program-alphafold-predicts-3d-shapes-of-proteins
Article Probabilistic multi-template protein homology modeling
Article Fast Protein Loop Sampling and Structure Prediction Using Di...
Preprint Distance-based Protein Folding Powered by Deep Learning
https://arxiv.org/abs/1802.00023
Regards,
Joachim
Thank you, Joachim, for your help. Indeed, the vast amount of algorithms I also came across in the field come from the area of AI. Having taken a look at your links made me realize that I did not narrow down the type of algorithms I am looking for in my question. Namely, I forgot to mention that I am interested primarily in ab initio algorithms, which are not template-based (no homology involved), hence my main focus lies on methods outside of machine learning. In my opinion ab initio is possibly the type that will allow us to understand the folding mechanism, however difficult that may be.
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