Protein engineering
is the discipline of developing useful proteins
for applications in research, therapeutic, and industrial processes
by modification of naturally occurring proteins or by invention of de novo proteins. Modern protein engineering relies on the
ability to rapidly generate and screen diverse libraries of mutant
proteins. However, design of mutant libraries is typically hampered
by scale and complexity, necessitating development of advanced automation
and optimization tools that can improve efficiency and accuracy. At
present, automated library design tools are functionally limited or
not freely available. To address these issues, we developed Mutation
Maker, an open source mutagenic oligo design software for large-scale
protein engineering experiments. Mutation Maker is not only specifically
tailored to multisite random and directed mutagenesis protocols, but
also pioneers bespoke mutagenic oligo design for de novo gene synthesis workflows. Enabled by a novel bundle of orchestrated
heuristics, optimization, constraint-satisfaction and backtracking
algorithms, Mutation Maker offers a versatile toolbox for gene diversification
design at industrial scale. Supported by in silico simulations and compelling experimental validation data, Mutation
Maker oligos produce diverse gene libraries at high success rates
irrespective of genes or vectors used. Finally, Mutation Maker was
created as an extensible platform on the notion that directed evolution
techniques will continue to evolve and revolutionize current and future-oriented
applications.
Founded on principles of natural selection, directed evolution techniques harness high-throughput gene diversification methodologies to generate proteins with optimized properties for applications in research, therapeutic and industrial processes. However, design of gene libraries is typically hampered by scale and complexity, necessitating development of advanced automation and optimization tools that can improve efficiency and accuracy. At present, automated library design tools are obsolete, functionally limited or not freely available for commercial use. To address these issues, we developed Mutation Maker, an open source mutagenic oligo design software for large-scale protein engineering experiments. Mutation Maker is not only specifically tailored to multi-site random and directed mutagenesis protocols, but also pioneers bespoke mutagenic oligo design for de novo gene synthesis workflows. Enabled by a novel bundle of orchestrated heuristics, optimization, constraint-satisfaction and backtracking algorithms, Mutation Maker offers a versatile toolbox for gene diversification design at industrial scale. Supported by in-silico simulations and compelling experimental validation data, Mutation Maker oligos produce diverse gene libraries at high success rates irrespective of genes or vectors used. Finally, Mutation Maker was created as an extensible platform on the notion that directed evolution techniques will continue to evolve and revolutionize current and future-oriented applications.
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