This chapter focuses on the application of computation tools to assist biocatalysis research. It introduces novel computational methods, which have been developed for the analysis and comparison of protein binding pockets and the estimation of energetic contributions of protein-protein and protein-ligand interactions, respectively. Novel in silico approaches, presented in the chapter, were developed in close cooperation with industrial partners, thereby allowing to concentrate on urgent problems in biocatalysis research. These novel methods comprise tools for the structural and functional analysis of enzymes as well as approaches to assist protein engineering tasks such as optimizing protein stability. Finally, the chapter comprises some of the biocatalysis questions. In the application of the computational tools, one of the most important questions in biocatalysis research, the annotation of the function of an enzyme, is addressed by the DoGSiteScorer support-vector machine (SVM)-based classification method. This question could be tackled by molecular docking.