Collaborative Research: ABI Development: Integrated platforms for protein structure and function predictions

合作研究：ABI开发：蛋白质结构和功能预测的集成平台

• 批准号: 2021734
• 负责人: Dukka KC
• 金额: $ 8.85万
• 依托单位: Wichita State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-01-07 至 2021-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2021734&HistoricalAwards=false
• 关键词: Collaborative; Research; ABI; Development; Integrated

Proteins are the 'workhorse' molecules of life, they participate in nearly every activity that cells carry out. It follows that understanding protein structure and function is essential to understanding life processes, and how to control or modify them. Biochemistry and biophysics experiments give the most accurate data on protein structure and function, but the experiments are often expensive and too specialized for many of the cell and molecular biologists focused on a particular interesting protein. This means that reliable computational predictions of protein structure and function are in high demand. These techniques are also specialized but can be automated, which is the focus of this project, which aims to develop an integrated platform for high-resolution protein structure prediction and structure-based function annotation that is accessible from the Web. This resource will significantly enhance studies of individual proteins as well as processes in cellular biology and other biological sciences. Through the collaboration of the two institutions, students at NCAT will learn state of the art high performance computing methods, and workshops at both institutions will provide greater understanding of the capabilities of the new resource. Proteins are complex components of biological systems, and studies on their structure and function often require multiple approaches to measurement or modeling. Many of the advanced computer algorithms used in this modeling are highly specialized, involving a number of complicated processes for each aspect of the protein modeling. Biologists whose primary interest is the final result often cannot determine which algorithm or pipeline to choose, how to enter parameters, or how to interpret the resulting models. While continuing to improve the accuracy of the core algorithms in protein structure prediction and structure-based function annotation, this project will also make improvements to domain parsing and assembly, to improve the quality of complex protein structure and function modeling. Another major focus of this project is to develop new protocols that automatically guide protein targets to the most suitable pipelines. In conjunction with this there will be new confidence scoring systems, both global and local, to assist biological users as they interpret the modeling results. In addition, advanced parallel computing and graphic processor unit techniques will be implemented in order to accelerate the pipelines and reduce user's waiting time. New opportunities will be made for improving educational outcomes, in particular for women and minority students, in both University of Michigan and the North Carolina A&T State University. The on-line protein modeling system will be accessible to the community at http://zhanglab.ccmb.med.umich.edu.

蛋白质是生命的“主力”分子，它们几乎参与细胞进行的每项活动。因此，了解蛋白质的结构和功能对于了解生命过程以及如何控制或修改它们至关重要。生物化学和生物物理学实验提供了有关蛋白质结构和功能的最准确数据，但这些实验通常成本高昂，而且对于许多专注于特定有趣蛋白质的细胞和分子生物学家来说过于专业。这意味着对蛋白质结构和功能的可靠计算预测的需求很高。这些技术也是专业化的，但可以自动化，这是该项目的重点，该项目旨在开发一个可从网络访问的高分辨率蛋白质结构预测和基于结构的功能注释的集成平台。该资源将显着加强对单个蛋白质以及细胞生物学和其他生物科学过程的研究。通过两个机构的合作，NCAT 的学生将学习最先进的高性能计算方法，两个机构的研讨会将让人们更好地了解新资源的功能。蛋白质是生物系统的复杂组成部分，对其结构和功能的研究通常需要多种测量或建模方法。该建模中使用的许多先进计算机算法都是高度专业化的，涉及蛋白质建模各个方面的许多复杂过程。主要兴趣是最终结果的生物学家通常无法确定选择哪种算法或流程、如何输入参数或如何解释生成的模型。在继续提高蛋白质结构预测和基于结构的功能注释等核心算法准确性的同时，该项目还将对域解析和组装进行改进，以提高复杂蛋白质结构和功能建模的质量。该项目的另一个主要重点是开发新的协议，自动引导蛋白质目标到最合适的管道。与此相结合的是，将有新的全局和本地置信度评分系统，以帮助生物用户解释建模结果。此外，还将实施先进的并行计算和图形处理器单元技术，以加速管道并减少用户的等待时间。 密歇根大学和北卡罗来纳州 A&T 州立大学将创造新的机会来改善教育成果，特别是女性和少数族裔学生的教育成果。社区可通过 http://zhanglab.ccmb.med.umich.edu 访问在线蛋白质建模系统。