quantum-protein-structure-prediction
Quantum algorithms for protein structure prediction. Language: Python (Qiskit). Platform: IBM Quantum's backends and simulators.
https://github.com/renatawong/quantum-protein-structure-prediction
Science Score: 67.0%
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Quantum algorithms for protein structure prediction. Language: Python (Qiskit). Platform: IBM Quantum's backends and simulators.
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README.md
Quantum algorithm for protein structure prediction
A Qiskit implementation of a quantum algorithm for protein structure prediciton in 2D hydrophobic-hydrophilic model. This notebook contains the accompanying code for the paper in [1].
Status
As of June 29, 2023, this notebook has been released by AWS on their GitHub repository platform as well as on the AWS Solutions Library: Quantum Computing Exploration for Drug Discovery on AWS.
Work is currently in progress on the accompanying code for [2].
Notes on use
For simplicity, this notebook requires the user to change manually the variable j specifying the expected energy (= number of hydrophobic-hydrophobic contacts in the lattice). The present value of j is 1 as this is the expected energy level for the amino acid sequence PHPPH (encoded as 01001).
Acknowledgement
This notebook is based on the theory described in [1].
The code was written by Renata Wong (https://renatawong.github.io/).
This work benefited greatly from discussions with Prof. Weng-Long Chang (National Kaohsiung University of Science and Technology) and Dr. Aoyu Zhang (AWS). All remaining deficiencies are my own.
References
[1] R. Wong and W-L. Chang. Fast quantum algorithm for protein structure prediction in hydrophobic-hydrophilic model, Journal of Parallel and Distributed Computing 164:178-190, 2022, DOI: 10.1016/j.jpdc.2022.03.011, https://www.sciencedirect.com/science/article/abs/pii/S0743731522000673.
[2] R. Wong and W-L. Chang. Quantum speedup for protein structure prediction, IEEE Transactions on Nanobioscience 20(3): 323-330, 2021. DOI: 10.1109/TNB.2021.3065051, https://ieeexplore.ieee.org/document/9374469.
Owner
- Name: Renata Wong
- Login: renatawong
- Kind: user
- Location: Poland / Taiwan
- Company: National Center for Theoretical Sciences, Taipei, Taiwan, R.O.C.
- Website: https://www.linkedin.com/in/renata-wong/
- Repositories: 4
- Profile: https://github.com/renatawong
Researcher in Quantum Information Science. IBM Certified Associate Developer (Quantum Computing). IBM Qiskit Advocate.
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Wong
given-names: Renata
orcid: https://orcid.org/0000-0001-5468-0716
title: "quantum algorithm for protein structure prediction"
version: 2.0.0
doi: N/A
date-released: 2023
url: "https://github.com/github/renatawong"
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