MULTI-SCALE VISUALIZATION OF LARGE MOLECULAR COMPLEXES

大分子复合物的多尺度可视化

• 批准号: 8363584
• 负责人: THOMAS GODDARD
• 金额: $ 2.79万
• 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/8363584
• 关键词: 3-Dimensional; Algorithms; Capsid; Cells; Chimera organism; Complex; Computer software; Databases; Encapsulated; Funding; Grant; Grouping; Image; Imagery; Informatics; Left; Modeling; Molecular; Molecular Models; National Center for Research Resources; Nucleic Acid Folding; Nucleic Acids; Planet Mars; Principal Investigator; Proteins; Publishing; Research; Research Infrastructure; Resolution; Resources; Ribosomes; Secondary to; Set protein; Source; Specific qualifier value; Structure; Surface; System; Tertiary Protein Structure; United States National Institutes of Health; Virion; Virus; Work; abstracting; animation; biocomputing; computer program; cost; macromolecule; molecular assembly/self assembly; molecular modeling; molecular shape; multi-scale modeling; software development; tool; web site

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 extensions to the UCSF Chimera molecular modeling package (http://www.cgl.ucsf.edu/chimera) for interactive visualization and analysis of large molecular assemblies such as viruses and ribosomes. These extensions facilitate studying atomic resolution models over a range of scales from atomic detail, to secondary structure (helices and sheets), to tertiary structure (protein and nucleic acid folds), to quaternary structure (packing of macromolecules to form an assembly). While many computer programs permit interactive exploration of small sets of protein or nucleic acid macromolecules, none work well with assemblies of 30 or more molecules. Known virus particle structures are composed of hundreds to thousands of molecules and are particularly difficult to study with existing software. The software we've developed focus on the quaternary structure level. The basic capabilities are encapsulated in the Multiscale Models tool. It allows representing molecules as simple surfaces that show overall molecular shape. This abstraction is needed for systems having hundreds of molecules. Applying symmetry is another basic capability. Most of the approximately 250 virus capsid structure have icosahedral symmetry. Only the asymmetric unit (1/60 of the capsid) is specified in atomic coordinate files. We are able to use the symmetry to display the entire capsid while only creating copies of the atomic coordinates when they are needed for displaying asymmetric units with differing styles and colorings. This is important for virus capsids which can contain millions atoms. In addition to abstract representations and symmetry handling, another challenge posed by large assemblies is in navigating to relevant subassemblies. For example, a virus capsid may have two layers each comprised of hundreds of proteins. A mechanism is needed to hide the outer layer so that the inner layer can be studied. Subassemblies such as virus capsid layers are in general not annotated in the Protein Databank files so defining these subassemblies is left to the user. Our multiscale extension permits navigating to subassemblies using user-defined molecule groupings. Details of the Multiscale Models tool were published in Goddard TD, Huang CC, Ferrin TE. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure (Camb). 2005 Mar;13(3):473-82. More advanced capabilites added in past years include an efficient algorithm for calculating atomic contacts between molecular components, the ability to show crystallographic unit cells, the ability to delete components, the ability to show transparent surfaces in combination with other molecular display styles, and ability to export 3 dimensional models for making animations. These capabilities have been used to create images for Virus Particle Explorer web site (http://viperdb.scripps.edu/) for all known icosahedral virus capsid structures.

该子项目是利用资源的众多研究子项目之一 由 NIH/NCRR 资助的中心拨款提供。子项目的主要支持 并且子项目的主要研究者可能是由其他来源提供的， 包括其他 NIH 来源。 子项目可能列出的总成本 代表子项目使用的中心基础设施的估计数量， NCRR 赠款不直接向子项目或子项目工作人员提供资金。 我们正在开发 UCSF Chimera 分子的软件扩展 用于交互式的建模包（http://www.cgl.ucsf.edu/chimera） 大分子组装体的可视化和分析，例如 病毒和核糖体。 这些扩展有助于学习原子 从原子细节到一系列尺度的分辨率模型 二级结构（螺旋和片状），到三级结构 （蛋白质和核酸折叠），到四级结构（包装 大分子形成组装体）。 虽然许多计算机程序 允许对小组蛋白质或核酸进行交互式探索 大分子，没有一个能很好地与 30 个或更多的组件配合使用 分子。 已知的病毒颗粒结构由数百个组成 涉及数千个分子，并且特别难以研究 现有软件。 我们开发的软件专注于四级结构水平。 基本功能封装在多尺度模型工具中。 它允许将分子表示为显示整体的简单表面 分子形状。 对于具有以下特征的系统来说需要这种抽象： 数百个分子。 应用对称性是另一个基本能力。 大约250种病毒衣壳结构中的大多数具有二十面体 对称。 仅指定不对称单元（衣壳的 1/60） 在原子坐标文件中。 我们可以利用对称性 显示整个衣壳，同时仅创建原子的副本 当需要显示不对称单位时的坐标 不同的风格和颜色。 这对于病毒衣壳很重要 它可以包含数百万个原子。 除了抽象 表示和对称处理，提出的另一个挑战 大型装配体正在导航到相关的子装配体。 为了 例如，病毒衣壳可能有两层，每层由数百个组成 蛋白质。 需要一种机制来隐藏外层，以便 可以研究内层。 病毒衣壳等子组件 蛋白质数据库文件中通常没有注释层，因此 定义这些子组件留给用户。 我们的多尺度 扩展允许使用用户定义导航到子装配体 分子分组。 多尺度模型工具的详细信息发布于 Goddard TD， 黄CC，费林TE。 UCSF chimera 的软件扩展 大分子组装体的交互式可视化。结构 （坎姆）。 2005 年 3 月；13(3)：473-82。 过去几年添加的更先进的功能包括高效的 计算分子之间原子接触的算法 组件，显示晶体晶胞的能力， 删除组件的能力，显示透明表面的能力 与其他分子显示样式相结合，并且能够 导出用于制作动画的 3 维模型。 这些功能已用于为病毒粒子创建图像 所有已知的资源管理器网站 (http://viperdb.scripps.edu/) 二十面体病毒衣壳结构。