Gate-based quantum computing for protein design

by Mohammad Hassan Khatami, Udson C. Mendes, Nathan Wiebe, Philip M. Kim

Protein design is a technique to engineer proteins by permuting amino acids in the sequence to obtain novel functionalities. However, exploring all possible combinations of amino acids is generally impossible due to the exponential growth of possibilities with the number of designable sites. The present work introduces circuits implementing a pure quantum approach, Grover’s algorithm, to solve protein design problems. Our algorithms can adjust to implement any custom pair-wise energy tables and protein structure models. Moreover, the algorithm’s oracle is designed to consist of only adder functions. Quantum computer simulators validate the practicality of our circuits, containing up to 234 qubits. However, a smaller circuit is implemented on real quantum devices. Our results show that using O(N) iterations, the circuits find the correct results among all N possibilities, providing the expected quadratic speed up of Grover’s algorithm over classical methods (i.e., O(N)).