title: Computational tools for designing and engineering biocatalysts.
abstract: Current computational tools to assist experimentalists for the design and engineering of proteins with desired catalytic properties are reviewed. The applications of these tools for de novo design of protein active sites, optimization of substrate access and product exit pathways, redesign of protein-protein interfaces, identification of neutral/advantageous/deleterious mutations in the libraries from directed evolution and stabilization of protein structures are described. Remarkable progress is seen in de novo design of enzymes catalyzing a chemical reaction for which a natural biocatalyst does not exist. Yet, constructed biocatalysts do not match natural enzymes in their efficiency, suggesting that more research is needed to capture all the important features of natural biocatalysts in theoretical designs.
authors.affiliation: Institute of Experimental Biology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic. jiri@chemi.muni.cz
authors.forename: Jiri
authors.initials: J
authors.lastname: Damborsky
authors.forename: Jan
authors.initials: J
authors.lastname: Brezovsky
mesh_terms: D055162:Biocatalysis; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D008024:Ligands; D009154:Mutation; D015202:Protein Engineering / Q000379:methods* / Q000639:trends; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D008024:Ligands; D011506:Proteins