Section I. Methodology -- Gene site saturation mutagenesis : a comprehensive mutagenesis approach -- Single-stranded DNA family shuffling -- Module shuffling -- SCHEMA-guided protein recombination -- Staggered extension process in vitro DNA recombination -- Using incremental truncation to create libraries of hybrid enzymes -- Random multirecombinant polymerase chain reaction -- Gene library synthesis by structure-based combinatorial protein engineering -- New enzymes from combinatorial library modules -- Construction of protein fragment complementation libraries using incremental truncation -- Section II. Applications: optimization and screening -- GigaMatrix: a novel ultrahigh throughput protein optimization and discovery platform -- High throughput microplate screens for directed protein evolution -- Periplasmic expression as a basis for whole cell kinetic screening of unnatural enzyme reactivities -- Engineering the thermotolerance and pH optimum of family 11 xylanases by site-directed mutagenesis -- Screening for oxidative resistance -- Consensus-based engineering of protein stability: from intrabodies to thermostable enzymes -- Improving the functional expression of N-Carbamoylase by directed evolution using the green fluorescent protein fusion reporter system -- Section III. Applications: directed evolution of enzymatic function -- Directed evolution of lipases and esterases -- Protein engineering of the cytochrome P450 monooxygenase from bacillus megaterium -- Directed evolution of aldolases -- Changing the enantioselectivity of enzymes by directed evolution -- Control of stereoselectivity in phosphotriesterase -- Section IV. Applications: evolution of biosynthetic pathways -- Manipulation and analysis of polyketide synthases -- Reactions catalyzed by mature and recombinant nonribosomal peptide synthetases -- Engineering carotenoid biosynthetic pathways -- Section V. Devices, antibodies, and vaccines -- Directed evolution of bacteriorhodopsin for device applications -- Engineering antibody affinity by yeast surface display -- A conditionally replicating virus as a novel approach toward an HIV vaccine.