VISUALIZATION SOFTWARE FOR ELECTRON MICROSCOPY

电子显微镜可视化软件

• 批准号: 8170522
• 负责人: THOMAS GODDARD
• 金额: $ 1.79万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8170522
• 关键词: 3-Dimensional; Chimera organism; Color; Computer Retrieval of Information on Scientific Projects Database; Computer software; Crystallography; Databases; Electron Microscopy; Filament; Funding; Grant; Institution; Life; Ligand Binding; Maps; Methods; Microtubules; Modeling; Molecular Machines; Molecular Models; Motor; Muscle; Organism; Proteins; Research; Research Personnel; Resolution; Resources; Ribosomes; Slice; Software Tools; Source; Structure; Surface; System; United States National Institutes of Health; Virus; Visualization software; Work; density; macromolecule; molecular assembly/self assembly; molecular modeling; software development

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We are developing software for interactively analyzing 3-dimensional density maps obtained by electron microscopy (EM). The analysis aims to determine structures and inner workings of molecular machines such as viruses, ribosomes, microtubules and motors, muscle filaments, and dozens of others systems that are targets of current research. It is believed that most proteins in living organisms are parts of large molecular assemblies. Advances in experimental methods in the past several years have greatly accelerated research on these systems. The primary database of EM density maps (http://www.ebi.ac.uk/msd-srv/emsearch/index.html) was founded in 2002 and now (2010) has 773 entries. Software for deducing structures from these maps is being actively developed by many labs. Our software displays contour surfaces of density maps. Maps from electron microscopy have resolutions in the 5 - 100 Angstrom range which is too coarse to see atomic detail. Analysis involves fitting known atomic structures from crystallography into the maps, identifying structures in maps corresponding to unidentified proteins, and comparing maps of the same system under different experimental conditions to deduce conformational changes or binding of ligands or specific macromolecules. Our software tools, which are part of the UCSF Chimera molecular modeling package, support fitting, carving out density regions, coloring maps, and building coarse models in maps. In the past we have added the ability to slice maps along an arbitrarily oriented and movable plane displaying density values on the cut surface.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 我们正在开发用于交互式分析 3 维的软件 通过电子显微镜（EM）获得的密度图。 分析目的 确定分子机器的结构和内部运作，例如 如病毒、核糖体、微管和马达、肌丝，以及 许多其他系统是当前研究的目标。 这是 相信生物体中的大多数蛋白质都是大分子的一部分 分子组装体。 以往实验方法的进展 几年来大大加速了对这些系统的研究。 这 电磁密度图的主要数据库 (http://www.ebi.ac.uk/msd-srv/emsearch/index.html) 成立于 2002 年 现在（2010 年）有 773 个条目。 用于推导结构的软件 许多实验室正在积极开发这些地图。 我们的软件显示密度图的轮廓表面。 地图来自 电子显微镜的分辨率在 5 - 100 埃范围内 这太粗糙，无法看到原子细节。 分析涉及拟合 从晶体学中已知的原子结构到图中， 识别图中对应于未识别蛋白质的结构， 并比较同一系统在不同实验下的图谱 推断构象变化或配体结合的条件或 特定的大分子。 我们的软件工具是 UCSF Chimera分子建模包，支撑拟合，雕刻 密度区域、着色地图以及在地图中构建粗略模型。 过去，我们添加了沿某个方向切片地图的功能 任意方向和可移动的平面，显示密度值 切割面。