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Gate-based quantum computing for protein design.

Mohammad Hassan Khatami1, Udson C Mendes2, Nathan Wiebe3,4,5

  • 1Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

Plos Computational Biology
|April 12, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a quantum computing approach using Grover's algorithm for protein design. This method offers a quadratic speedup over classical techniques for exploring protein sequence possibilities.

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Area of Science:

  • Computational Biology
  • Quantum Computing
  • Biochemistry

Background:

  • Protein design aims to create novel protein functionalities by altering amino acid sequences.
  • The combinatorial complexity of protein design limits classical computational exploration.
  • Quantum computing offers a potential avenue for accelerating complex computational problems.

Purpose of the Study:

  • To develop and validate quantum circuits for protein design using Grover's algorithm.
  • To demonstrate the feasibility of a pure quantum approach for exploring protein sequence space.
  • To achieve a quadratic speedup compared to classical protein design methods.

Main Methods:

  • Implementation of Grover's algorithm on quantum circuits tailored for protein design.
  • Adaptation of algorithms for custom pair-wise energy tables and protein structure models.
  • Design of a quantum oracle utilizing only adder functions for efficiency.

Main Results:

  • Quantum circuits were validated on simulators up to 234 qubits, with smaller circuits tested on real quantum devices.
  • The quantum approach successfully identified correct protein design solutions.
  • A quadratic speedup was observed, consistent with Grover's algorithm's theoretical performance.

Conclusions:

  • Quantum computing, specifically Grover's algorithm, presents a viable and efficient method for tackling the combinatorial challenges in protein design.
  • The developed quantum circuits are adaptable to various protein models and energy functions.
  • This work paves the way for leveraging quantum computation in protein engineering and drug discovery.