Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age

Abstract

The study of natural enzyme catalytic processes at a molecular level can provide essential information for a rational design of new enzymes, to be applied in more efficient and environmentally friendly industrial processes. The use of computational tools, combined with experimental techniques, is providing outstanding milestones in the last decades. However, apart from the complexity associated with the nature of these large and flexible biomolecular machines, the full enzyme catalyzed process involves different physical and chemical steps. Consequently, from the computational point of view, a deep understanding of every single step requires the selection of a proper computational technique to get reliable, robust and useful results. In this article, we summarize the different computational techniques and their use in the study of every single step of the catalytic process, including conformational diversity, allostery and those to study the chemical steps, as well as in the design of new enzymes. Because of the impact of artificial intelligence in all aspects of science during the last years, special attention has been applied to methods based on these techniques, their foundations and some selected recent applications.