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We describe a directed evolution approach that should find broad application in generating enzymes that meet predefined process-design criteria. It augments recombination-based directed evolution by incorporating a strategy for statistical analysis of protein sequence activity relationships (ProSAR). This combination facilitates mutation-oriented enzyme(More)
The avermectin analog doramectin (CHC-B1), sold commercially as Dectomax, is biosynthesized by Streptomyces avermitilis. aveC, a gene encoding an unknown mechanistic function, plays an essential role in the production of doramectin (avermectin CHC-B1), modulating the production ratio of CHC-B1 to other avermectins, most notably the undesirable analog(More)
Automated code generation is the process whereby a computer program takes user specifications in some form and produces a program as output. Automated code generation can be the process undertaken by a compiler, which generates an executable program from a source program, but it also applies to the situation where the input is a task described at some level(More)
Directed evolution is a powerful tool for the creation of commercially useful enzymes, particularly those approaches that are based on in vitro recombination methods, such as DNA shuffling. Although these types of search algorithms are extraordinarily efficient compared with purely random methods, they do not explicitly represent or interrogate the(More)
An in silico protein model based on the Kauffman NK-landscape, where N is the number of variable positions in a protein and K is the degree of coupling between variable positions, was used to compare alternative search strategies for directed evolution. A simple genetic algorithm (GA) was used to model the performance of a standard DNA shuffling protocol.(More)
Recent attention has been paid to the inadequacy of using the ratio Vmax/KM as a measure of enzyme performance, particularly in the context of industrial biocatalysis. This can lead to misleading expectations of enzyme performance and can be troublesome when used to select among different variants for scale-up evaluation under process conditions. To address(More)
Alternative search strategies for the directed evolution of proteins are presented and compared with each other. In particular, two different machine learning strategies based on partial least-squares regression are developed: the first contains only linear terms that represent a given residue's independent contribution to fitness, the second contains(More)