title: Strategies and computational tools for improving randomized protein libraries.
abstract: In the last decade, directed evolution has become a routine approach for engineering proteins with novel or altered properties. Concurrently, a trend away from purely 'blind' randomization strategies and towards more 'semi-rational' approaches has also become apparent. In this review, we discuss ways in which structural information and predictive computational tools are playing an increasingly important role in guiding the design of randomized libraries: web servers such as ConSurf-HSSP and SCHEMA allow the prediction of sites to target for producing functional variants, while algorithms such as GLUE, PEDEL and DRIVeR are useful for estimating library completeness and diversity. In addition, we review recent methodological developments that facilitate the construction of unbiased libraries, which are inherently more diverse than biased libraries and therefore more likely to yield improved variants.
authors.affiliation: Center for Fundamental and Applied Molecular Evolution, Emory University, 1510 Clifton Road, Atlanta GA 30322, USA. wpatric@emory.edu
authors.forename: Wayne M
authors.initials: WM
authors.lastname: Patrick
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Firth
mesh_terms: D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D019020:Directed Molecular Evolution; D005656:Fungal Proteins / Q000737:chemistry; D015723:Gene Library; D014644:Genetic Variation; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D008968:Molecular Conformation; D016296:Mutagenesis; D009154:Mutation; D009841:Oligonucleotides / Q000737:chemistry; D016133:Polymerase Chain Reaction; D015202:Protein Engineering / Q000379:methods*; D047428:Protein Kinase Inhibitors / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D011995:Recombination, Genetic; D012984:Software
chemical_list: D001426:Bacterial Proteins; D005656:Fungal Proteins; D009841:Oligonucleotides; D047428:Protein Kinase Inhibitors; D011506:Proteins