Enzyme Modeling: From the Sequence to the Substrate Complex

This chapter gives an overview on computational methods to study the relationship between sequence, structure, and function of proteins. Computational methods are in widespread use to search for novel enzymes with the desired properties in sequence and structure databases and to guide enzyme engineering toward variants with improved properties. The structure and function of enzymes can be modeled by two complementary methods, namely, data-driven modeling and mechanistic modeling. The integration of both methods allows the discovery of novel enzymes and the improvement of known enzymes by amino acid exchanges. Because the costs of DNA sequencing of whole genomes and metagenomes are exponentially decreasing, predicting structure and function of proteins from their sequence is a promising route toward novel bioprocesses.