Quantum algorithm for bioinformatics to compute the similarity between proteins

Abstract

Drug discovery has become a main challenge in the society, following the COVID-19 pandemic. However, pharmaceutical companies are already using computing to accelerate drug discovery and are increasingly interested in quantum computing (QC), with a view to improving the speed of development process for new drugs. The authors propose a quantum method for generating random sequences based on occurrence in a protein database and quantum algorithms for calculating a similarity rate between proteins. Both concepts can be used for structure prediction in drug design. The aim is to find the proteins closest to the generated protein and obtain an ordering of these proteins. First, the authors will present the construction of a quantum protein generator that defines a protein, called a test protein. The authors will then describe different methods to compute the similarity's rate between each protein in the database and the test protein or, for a case study, the elafin. The algorithms have been extended or adapted to a quantum formalism for use cases, that is, amino acid sequences, and tested to see the added value of quantum versions. The interest is to observe whether QC can be used in the drug discovery process.