SBIR Phase I: Software for high-throughput combinatorial design and curation of novel proteins

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) project is to enable scientists to design protein constructs using high throughput protein engineering to obtain the exact biological tools they need for a particular experiment by purchasing synthetic DNA coding for these proteins from a DNA synthesizer easily and economically. Currently, researchers using proteins as biological tools in their experiments expend significant time, effort and money to design and manually build these proteins - and too often that cost is so high that researchers settle for using a tool that is less than optimal for their experimental purposes. Ensuring broad biological applicability of an experiment requires correct controls, both positive and negative, as well as multiple interrogation strategies that must each be validated. Without satisfying these requirements, an experiment's applicability may be narrower than desired. In today's experimental landscape where proteins are used as biological tools, there are technical hurdles that make broad applicability difficult to achieve. This proposal aims to reduce these technical barriers by enabling scientists to design and economically obtain a logically complete set of protein tools in a way that allows them to logically optimize their experiments. Further, by functionally annotating these designs, a scientist will be able to rapidly disseminate those details to other scientists. This SBIR Phase I project proposes to develop software for scientists to design and curate combinatorial libraries of novel proteins so that DNA can be directly ordered from DNA synthesis companies. The purpose of this software is to enable a scientist to design and purchase a logically complete set of proteins that promotes the broad biological applicability of their experiment. Today, synthetic DNA suppliers are developing the ability to manufacture combinatorial libraries of DNA sequences at economical prices. However, there is currently no efficient means to design such a library for manufacture that matches the DNA synthesizers' capabilities with a protein engineer's experimental requirements. This software aims to structure the scientist's designs as a computationally complex recipe for amino acid products that can be expressed to a DNA synthesizer in a way that matches their manufacturing capabilities. This software will follow computational rules for generating biologically reasonable proteins from a recipe of components. It will then transmit the resulting data to DNA synthesizers. In addition, it will provide a straightforward user-interface for researchers to evaluate and designate the functionality of the generated proteins so that others may learn from their designs.