Predicting antibody structure plays a central role in drug development. The structural region responsible for most of the binding and function of an antibody, namely the H3 loop, is also the most variable and hard to predict to atomic accuracy. The desire to facilitate and accelerate the engineering of therapeutic antibodies has led to the development of computational methodologies aimed at antibody and H3 loop structure prediction. However, such approaches can be computationally demanding and time consuming, and still limited in their prediction accuracy. While quantum computing has been recently proposed for protein folding problems, antibody H3 loop modelling is still unexplored. In this paper we discuss the potential of quantum computing for fast and high-accuracy loop modelling with possible direct applications to pharmaceutical research. We propose a framework based on quantum Markov chain Monte Carlo for modelling H3 loops on a fault-tolerant quantum computer, and estimate the resources required for this algorithm to run. Our results indicate that further improvements in both hardware and algorithm design will be necessary for a practical advantage to be realized on a quantum computer. However, beyond loop modelling, our approach is also applicable to more general protein folding problems, and we believe that the end-to-end framework and analysis presented here can serve as a useful starting point for further improvements.
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