Directed evolution is the overall framework that can lead to the engineering of such proteins. Moreover, screening has to be performed in a quantitative fashion to help guide the process of directed evolution. We have found that high throughput flow cytometry is a very powerful tool for library screening. We have developed versatile systems for the isolation of proteins that bind to ligands and new enzymes using flow cytometry with appropriate substrates. The latter is particularly important since it is not feasible to screen large protein libraries for enzyme activity with any other means.
Research strongly suggests that natural diversity is the preferred source.
In cases where natural diversity is not available we have used other diversity. Because we can optimize small positions in any single cycle, performing multiple positions is essential for improvement. Our results have shown that recombination of DNA is the best method to go from cycle to cycle. A pool of one cycle is pooled to create a much larger screen of diversity. The mutation that is good in cycle 3 might not be good in cycle 30.