ArticleApplied and environmental microbiology2012
When second best is good enough: another probabilistic look at saturation mutagenesis.
Article in Applied and environmental microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
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- Generation of a CDR H3 Randomized Monoclonal Antibody Library by Kunkel Mutagenesis.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Sampling Strategies for Experimentally Mapping Molecular Fitness Landscapes Using High-Throughput Methods.Journal of molecular evolution · 2024Article
- Deep mutational scanning of proteins in mammalian cells.Cell reports methods · 2023Review
- Divergent directed evolution of a TetR-type repressor towards aromatic molecules.Nucleic acids research · 2023Article
- Directed evolution of angiotensin-converting enzyme 2 peptidase activity profiles for therapeutic applications.Protein science : a publication of the Protein Society · 2023Article
- Automating the High-Throughput Screening of Protein-Based Optical Indicators and Actuators.Biochemistry · 2023Review
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Abstract
We developed new criteria for determining the library size in a saturation mutagenesis experiment. When the number of all possible distinct variants is large, any of the top-performing variants (e.g., any of the top three) is likely to meet the design requirements, so the probability that the library contains at least one of them is a sensible criterion for determining the library size. By using a criterion of this type, one may significantly reduce the library size and thus save costs and labor while minimally compromising the quality of the best variant discovered. We present the probabilistic tools underlying these criteria and use them to compare the efficiencies of four randomization schemes: NNN, which uses all 64 codons; NNB, which uses 48 codons; NNK, which uses 32 codons; and MAX, which assigns equal probabilities to each of the 20 amino acids. MAX was found to be the most efficient randomization scheme and NNN the least efficient. TopLib, a computer program for carrying out the related calculations, is available through a user-friendly Web server.
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