ABI: A Toolbox for Large-Scale Analysis of Structural Molecular Data

william Marsh Rice大学获得一项资助，设计并实现一个可扩展的、计算效率高的工具箱，该工具箱将序列信息和现有的分子元数据与蛋白质结构分析集成在一起。现代生物学中最具挑战性的任务之一是解释通过最近的基因组学，蛋白质组学和相关进展获得的大量数据。蛋白质是细胞的工作分子，因此人们对了解它们的行为、相互关系以及它们如何调节生理过程有着极大的兴趣。工具箱的核心是一种快速且可扩展的子结构匹配方法，该方法可以找到一组三维原子（基序）与一组蛋白质结构的对应关系。其目标是为生物学家提供一种多功能的“瑞士军刀”，用于探索蛋白质结构和功能之间的关系。该工具箱的构建方式将自动从相关的在线数据库中提取元数据信息，以便持续更新。输出不仅将报告和可视化结果，还将链接到在线资源以进行进一步的评估和分析。该项目更广泛的影响将通过提供一个多功能的计算工具箱来分析蛋白质结构和功能，从而加强生物基础设施。该工具箱将广泛传播(1)作为web服务，(2)作为带有命令行和Python模块接口的可下载包，以及(3)作为流行的免费分子建模程序Chimera的插件。除了与合作者合作外，pi还将与兴趣团体和相关会议联系，为拟议的工具建立一个用户社区，并鼓励科学界贡献新的工作流程。参与该项目的学生将作为一个高度跨学科团队的一部分接受培训，并计划为本科生举办教育和研究活动（通过计算机研究协会妇女在计算机研究中的地位委员会）。

A Toolbox for Large-Scale Analysis of Structural Molecular DataWilliam Marsh Rice University is awarded a grant to design and implement an extensible and computationally efficient toolbox that integrates sequence information and existing molecular metadata with structural analysis of proteins. One of the most challenging tasks in modern biology is the interpretation of the massive amounts of data becoming available through recent genomics, proteomics and related advances. Proteins are the cell's worker molecules, so there is a tremendous interest to understand how they behave, relate to each other, and how they regulate physiological processes. At the core of the toolbox is a fast and scalable substructure matching method that finds correspondences of a three-dimensional set of atoms (a motif) to a set of protein structures. The goal is to provide biologists with a versatile 'Swiss army knife' for probing the relationship between protein structure and function. The toolbox will be built in a way that it will automatically draw metadata information from relevant online databases in order to be continuously up-to-date. The output will not only report and visualize the results but link to online sources for further evaluation and analysis. The broader impacts of this project will strengthen biological infrastructure by providing a versatile computational toolbox for the analysis of protein structure and function. The toolbox will be widely disseminated (1) as a web service, (2) as a downloadable package with a command line and Python module interface, and (3) as a plug-in for Chimera, a popular, free molecular modeling program. Besides working with their collaborators, the PIs will reach out to interest groups and related conferences for building a community of users for the proposed tool and encourage the contribution of novel workflows by the scientific community. Students involved in the project will be trained as part of a highly interdisciplinary team, and educational and research activities (through CRA-W, the Computer Research Association's Committee on the Status of Women in Computing Research) for undergraduate students are planned.