VISUALIZING SYMMETRIC MOLECULAR MODELS AT THE PROTEIN DATA BANK

在蛋白质数据库中可视化对称分子模型

• 批准号: 7723544
• 负责人: THOMAS GODDARD
• 金额: $ 1.54万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-07-01 至 2009-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723544
• 关键词: Capsid; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer software; Data; Databases; Detection; Funding; Grant; Imagery; Institution; Modeling; Molecular Structure; Protein Subunits; Proteins; Research; Research Personnel; Resources; Source; System; To specify; United States National Institutes of Health; Virus; Writing; X-Ray Diffraction; molecular assembly/self assembly; molecular modeling; software development; tool

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. This project develops software for the Protein Data Bank for visualizing and validating structures of molecular complexes containing tens to thousands of molecules. The initial aim of the project was to correct errors in the symmetry matrices used to specify virus capsid assemblies. The symmetry specifications in Protein Data Bank virus models used a variety of undocumented coordinate systems and omitted data or include incorrect symmetries, mistakes that were difficult to catch because no readily available tools used that information. Software has been written to view the molecular assemblies using the symmetry information in PDB files and also to detect and display severe clashes between protein subunits of such models that may indicate incorrect symmetry. The capabilities have been extended to validate crystallographic symmetry that describes the packing of biomolecules in crystals used for xray diffraction. Refinements to the symmetry visualization and clash detection are ongoing.

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 该项目为蛋白质数据库开发软件，用于可视化和验证包含数万到数千个分子的分子复合体的结构。该项目的最初目标是纠正用于确定病毒衣壳组装的对称矩阵中的错误。蛋白质数据库病毒模型中的对称性规范使用了各种未记录在案的坐标系，并省略了数据或包含了不正确的对称性，这些错误很难被发现，因为没有现成的工具使用这些信息。已经编写了软件来使用PDB文件中的对称信息来查看分子组装，还可以检测和显示这类模型的蛋白质亚单位之间可能表明不正确对称性的严重冲突。这些能力已经扩展到验证晶体对称性，该对称性描述了用于X射线衍射的晶体中生物分子的堆积。对对称可视化和碰撞检测的改进正在进行中。