VISUALIZATION SOFTWARE FOR ELECTRON MICROSCOPY

电子显微镜可视化软件

• 批准号: 8363597
• 负责人: THOMAS GODDARD
• 金额: $ 1.68万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363597
• 关键词: 3-Dimensional; Chimera organism; Color; Computer software; Crystallography; Databases; Electron Microscopy; Filament; Funding; Grant; Imagery; Informatics; Life; Ligand Binding; Maps; Methods; Microtubules; Modeling; Molecular Machines; Molecular Models; Motor; Muscle; National Center for Research Resources; Organism; Principal Investigator; Proteins; Research; Research Infrastructure; Resolution; Resources; Ribosomes; Slice; Software Tools; Source; Structure; Surface; System; United States National Institutes of Health; Virus; Visualization software; Work; biocomputing; cost; density; indexing; 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. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 我们正在开发交互式分析三维的软件 通过电子显微镜（EM）获得的密度图。 分析目的 来确定分子机器的结构和内部工作方式， 如病毒、核糖体、微管和马达、肌丝， 几十个其他的系统是目前研究的目标。 是 认为生物体中的大多数蛋白质都是 分子组装 过去实验方法的进展 几年来大大加快了对这些系统的研究。 的 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。 地图从 电子显微镜的分辨率在5 - 100埃范围内 这太粗糙了，无法看到原子细节。 分析涉及拟合 已知的原子结构从晶体学到地图上， 识别对应于未识别蛋白质的图谱中的结构， 并对同一系统在不同实验条件下的图谱进行了比较 推断配体的构象变化或结合的条件， 特定的大分子。 我们的软件工具是 UCSF Chimera分子建模包，支持拟合，雕刻 密度区域、着色地图以及在地图中构建粗糙模型。 在过去，我们添加了沿沿着 显示密度值的任意方向和可移动的平面 切割表面。