Integrated Resource for Protein Recognition Studies

蛋白质识别研究综合资源

• 批准号: 7019180
• 负责人: ILYA VAKSER
• 金额: $ 23.66万
• 依托单位: UNIVERSITY OF KANSAS LAWRENCE
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-03-01 至 2009-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7019180
• 关键词: Internet; bioinformatics; computational biology; crystallization; genome; model; molecular biology information system; protein protein interaction; protein structure function; structural biology; technology /technique development

DESCRIPTION (provided by applicant): The protein-protein docking problem is one of the focal points of activity in computational structural biology. The 3D structure of a protein-protein complex, generally, is more difficult to determine experimentally than the structure of an individual protein. Adequate computational techniques to model protein interactions are important because of the growing number of known protein 3D structures, particularly in the context of structural genomics. The project will improve our understanding of fundamental properties of protein interaction and will facilitate development of better tools for prediction of protein complexes. The Specific Aims of the project are: (1) development of an advanced docking algorithm, (2) database of protein-protein co-crystallized structures, (3) database of protein-protein simulated unbound structures, (4) database of protein-protein models, (5) database of docking decoys, and (6) integrated web-based public resource for studying protein recognition. The long-term goals are: (a) development of an automated tool for a reliable modeling of protein interactions, which will account for dynamic changes in the molecular structures and kinetics of protein association and (b) utilization of this tool to understand principles of protein interaction. The ultimate goal is to recreate the network of protein interactions in genomes and understand the structure-base mechanisms of these interactions. The systematic, detailed description of these interactions will provide insights into the basic principles of life processes at the molecular level. The focus of the proposal is an integrated system of resources for studying protein-protein 3D interactions. An existing docking procedure will be developed further to make it more adequate to the challenges of structural modeling of protein-protein complexes. The procedure will be used to generate the docking datasets for the development of modeling capabilities. The core dataset will consist of co-crystallized protein-protein structures. The dataset will have options to exclude redundancies based on sequence and structure similarities. It will be regularly updated and annotated. The database of simulated unbound complexes will be built upon the core dataset. It will serve as a comprehensive benchmark set for the development of docking techniques. The database of protein-protein models will provide a unique expansion of the core dataset for development of docking capabilities in protein modeling, including genome-wide studies. The database of docking decoys will provide the community-wide testing ground for new scoring functions.

描述（由申请人提供）：蛋白质 - 蛋白质对接问题是计算结构生物学活动的焦点之一。通常，蛋白质蛋白质复合物的3D结构比单个蛋白质的结构更难在实验上确定。建模蛋白质相互作用的足够计算技术很重要，因为已知的蛋白质3D结构数量越来越大，特别是在结构基因组学的背景下。该项目将提高我们对蛋白质相互作用的基本特性的理解，并将促进更好地预测蛋白质复合物的工具。 The Specific Aims of the project are: (1) development of an advanced docking algorithm, (2) database of protein-protein co-crystallized structures, (3) database of protein-protein simulated unbound structures, (4) database of protein-protein models, (5) database of docking decoys, and (6) integrated web-based public resource for studying protein recognition.长期目标是：（a）开发自动化工具，用于对蛋白质相互作用的可靠建模，这将解释分子结构的动态变化和蛋白质关联的动力学，以及（b）利用该工具来了解蛋白质相互作用的原理。最终目标是重现基因组中蛋白质相互作用的网络，并了解这些相互作用的结构基机制。这些相互作用的系统，详细的描述将提供有关分子层面生命过程的基本原理的见解。该提案的重点是用于研究蛋白质 - 蛋白质3D相互作用的集成资源系统。将进一步开发现有的对接程序，以使其更加应对蛋白质 - 蛋白质复合物结构建模的挑战。该过程将用于生成对接数据集以开发建模功能。核心数据集将由共结晶的蛋白质 - 蛋白质结构组成。该数据集将具有根据序列和结构相似性排除冗余的选项。它将定期更新和注释。模拟未结合复合物的数据库将在核心数据集上构建。它将作为开发对接技术的全面基准设置。蛋白质蛋白质模型的数据库将为核心数据集提供独特的扩展，以开发蛋白质建模中的对接功能，包括全基因组研究。对接诱饵的数据库将为新的评分功能提供社区范围内的测试场。