OptZyme (2013): Enzyme redesign through the use of transition state analogues
Despite the growing availability of this high-throughput data, we still know very little about the metabolic contributions of individual microbial players within an ecological niche and the extent and directionality of metabolic interactions among them. This calls for development of efficient modeling frameworks to elucidate less understood aspects of metabolism in microbial communities.
OptZyme is used to redesign enzymes with optimized catalytic properties after identifying the relevant substrates and transition state analogues. Transition state analogue compounds are used as a substitute for typically unknown transition state structures. Optimized enzyme mutants are identified using our IPRO procedure. Restraints can be imposed to retain catalytic functionality.
The code is freely available for academic users. Before downloading our software, we ask for your name and institution so we may better design future versions of our software. Every consideration has been made during the design, writing, and posting of this code to ensure the program works properly.