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Where I can read about protein folding on quantum computer (Qiskit will be ideal variant) with simple examples? Thanks

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  • $\begingroup$ @mark-fingerhuth of ProteinQure is on this $\endgroup$
    – AHusain
    Jul 8, 2019 at 18:21
  • $\begingroup$ The general term for simulating physical systems on a quantum computer is "Hamiltonian simulation" $\endgroup$
    – ahelwer
    Jul 9, 2019 at 20:20

4 Answers 4

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Have a look at this recently published paper presenting a protein folding quantum algorithm. This work was done using Qiskit and the algorithm will soon be published as part of the new Qiskit Nature package.

EDIT: Here are the protein folding module in Qiskit Nature and the corresponding tutorial.

EDIT 2: EDIT: The links to the Qiskit module is now deprecated. Here is what is available now.

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From a more fault-tolerant perspective, https://arxiv.org/abs/2101.10279 also tackles this problem.

Disclaimer: I am one of the authors :)

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Qiskit has already a tutorial on protein folding using Qiskit Nature: Qiskit Nature tutorials - protein folding

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For a short background on protein folding, there are 4 letters in the RNA alphabet:

$$A, U, G,C$$

Each 3 consecutive letters from the RNA alphabet code for an amino acid, eg.

$$\{UUUACAGCU\}_{RNA} \rightarrow \{PTA\}_{amino-acid}$$

There are 20 amino acids that are standard in Earth biology,

$$A, R, N, D, C, E, A, G, H, I, L, K, M, F, P, S, T, W, Y, V$$

A "protein" is a long enough chain ($\gt 20$) of amino acids, eg.

$$\{ACDDGHHWYTSSPFENNNRST\}_{amino-acid} \rightarrow X_{Protein}$$

Quite remarkably, the same chain composition will fold into the same 3 dimensional shape most of the time (in similar external environment).

Misfolding of amino acid chains is thought to be responsible for some serious diseases (eg, Alzheimer's).

The adiabatic search space of a simple-model chain of only 9 amino acids (in 2 dimensions) is already

$$2^{81}$$

which is far beyond exhaustive classical optimizations.

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