SBIR Phase I: Software for High-Throughput Combinatorial Design and Curation of Novel Proteins

SBIR 第一阶段：用于新型蛋白质的高通量组合设计和管理的软件

• 批准号: 1548676
• 负责人: Justin Farlow
• 金额: $ 15万
• 依托单位: Serotiny, Inc.
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-01-01 至 2016-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1548676&HistoricalAwards=false
• 关键词: SBIR; Phase; Software; Throughput; Combinatorial

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.

这个小企业创新研究（SBIR）项目的更广泛的影响/商业潜力是使科学家能够使用高通量蛋白质工程设计蛋白质构建体，以获得特定实验所需的精确生物工具，方法是从DNA合成仪轻松经济地购买编码这些蛋白质的合成DNA。 目前，在实验中使用蛋白质作为生物工具的研究人员花费了大量的时间，精力和金钱来设计和手动构建这些蛋白质-而且往往成本如此之高，以至于研究人员满足于使用不适合其实验目的的工具。 确保实验的广泛生物适用性需要正确的控制，无论是阳性还是阴性，以及必须验证的多种询问策略。 如果不满足这些要求，实验的适用性可能比期望的要窄。在今天的实验环境中，蛋白质被用作生物工具，存在技术障碍，难以实现广泛的适用性。该提案旨在减少这些技术障碍，使科学家能够设计和经济地获得一套逻辑上完整的蛋白质工具，使他们能够在逻辑上优化他们的实验。 此外，通过对这些设计进行功能注释，科学家将能够迅速将这些细节传播给其他科学家。SBIR第一阶段项目提出开发软件，供科学家设计和管理新蛋白质的组合文库，以便可以直接从DNA合成公司订购DNA。该软件的目的是使科学家能够设计和购买一套逻辑上完整的蛋白质，以促进其实验的广泛生物适用性。今天，合成DNA供应商正在开发以经济的价格制造DNA序列组合文库的能力。然而，目前还没有有效的方法来设计这样一个用于制造的文库，该文库将DNA合成器的能力与蛋白质工程师的实验要求相匹配。 该软件旨在将科学家的设计结构化为氨基酸产品的计算复杂配方，这些氨基酸产品可以以与其制造能力相匹配的方式表达给DNA合成仪。该软件将遵循计算规则，从成分配方中生成生物合理的蛋白质。 然后，它将把产生的数据传输到DNA合成器。 此外，它将为研究人员提供一个简单的用户界面，以评估和指定所生成蛋白质的功能，以便其他人可以从他们的设计中学习。