Modeling and Interacting with the Visible Molecular Cell

可见分子细胞建模并与之交互

• 批准号: 9532908
• 负责人: DAVID S GOODSELL
• 金额: $ 47.34万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-15 至 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9532908
• 关键词: Address; Appearance; Bacteria; Bacterial Model; Biological Models; Biology; Cell model; Cell physiology; Cells; Cellular biology; Collaborations; Complex; Computer Assisted; Computer software; Crowding; Data; Data Set; Databases; Development; Disease; Education; Education and Outreach; Educational Curriculum; Environment; Escherichia coli; Genomics; Goals; HIV; Imagery; Intervention; Lipopolysaccharides; Membrane; Methods; Modeling; Molecular; Organism; Peptidoglycan; Pilot Projects; Planet Earth; Polyribosomes; Proteomics; Recipe; Research; Research Personnel; Resolution; Running; Scientist; Specialist; Specific qualifier value; Structural Models; Structure; Technology; Time; Viola; Visualization software; Work; base; crosslink; fluorescence imaging; method development; molecular assembly/self assembly; outreach; prototype; simulation; three-dimensional modeling; tool

Project Summary/Abstract It is now possible to approach the structural modeling and visualization of entire cells with detail at the atomic level. In this project, we will expand the capabilities of cellPACK, a method for creating integrative 3D models of cellular environments, bridging from the level of atoms to the level of cells. These models will provide unprecedented possibilities for the understanding of cellular function and disease states, enabling new opportunities for intervention. They will also challenge several aspects of the technologies needed to generate, visualize and interactively explore very large 3D and 4D structural datasets. Our goal is to develop the modeling and visualization tools that enable others to develop, run and analyze dynamic simulations of these complex models. Several critical barriers must be overcome to make this effort a successful tool for research and scientific education, including the management of large informational databases, methods for the automated modeling of the structure and interaction of soluble, fibrous, and membrane-bound molecular assemblies in crowded cellular environments, and comprehensible visualization of, and interaction with these large and heterogenous models. We will approach these challenges with four specific aims: 1) Procedural methods for mesoscale modeling of complex assemblies, such as the bacterial nucleoid, peptidoglycan, lipopolysaccharide, and polysomes; 2) Computer-assisted tools for the management of complex multiscale data for specifying 3D mesoscale models of cells; 3) Development of fast and effective methods to allow display of and interaction with these complex mesoscale models; 4) Application of these methods to research in bacterial biology and creation of a Google Earth inspired viewer for use in education and outreach.

项目摘要/摘要 现在可以接近整个细胞的结构建模和可视化 在原子水平上有细节。在这个项目中，我们将扩展 CellPack，一种创建蜂窝环境的集成3D模型的方法， 从原子水平桥接到细胞水平。这些模型将提供 理解细胞功能和疾病状态的前所未有的可能性， 为干预带来新的机会。他们还将挑战 生成，可视化和交互式探索非常大的3D所需的技术 和4D结构数据集。我们的目标是开发建模和可视化工具 这使其他人能够开发，运行和分析这些复杂的动态模拟 型号。必须克服几个关键障碍，以使这项努力成为成功的工具 用于研究和科学教育，包括大量信息的管理 数据库，结构结构自动建模的方法 拥挤的细胞中的可溶性，纤维和膜结合的分子组件 环境，以及可视化的可视化以及与这些大型和 异质模型。我们将以四个具体的目标应对这些挑战： 1）用于复杂组件的中尺度建模的程序方法，例如 细菌核苷，肽聚糖，脂多糖和多糖浆； 2）用于管理复杂多尺度数据的计算机辅助工具 指定细胞的3D中尺度模型； 3）开发快速有效的方法，以显示和与 这些复杂的中尺度模型； 4）这些方法在细菌生物学研究和Google的创建中的应用 地球启发了观众在教育和宣传中使用。