Icosahedral Particle Reconstruction Software

二十面体粒子重建软件

• 批准号: 6758168
• 负责人: Wah Chiu
• 金额: $ 22.58万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-05-01 至 2007-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6758168
• 关键词: Internet; bioimaging /biomedical imaging; chemical models; computational biology; computer human interaction; computer program /software; computer simulation; computer system design /evaluation; enzyme structure; image enhancement; interactive multimedia; mathematical model; particle; protein structure; three dimensional imaging /topography; virus morphology

DESCRIPTION (provided by applicant): Many spherical viruses and some enzyme complexes form particles having icosahedral symmetry. The use of electron cryomicroscopy and single particle reconstruction has allowed us to visualize the 3-dimensional structures of this type of particle to 7-9 A resolution. This resolution is sufficient to resolve long alpha helices and recognize large beta sheets. In the past three years, we have determined 6 structures of icosahedral particles with sizes ranging from 600 -1250 A in this resolution range. They include herpesvirus capsid, rice dwarf virus, procapsid and mature forms of P22 bacteriophage, rotavirus and cytoplasmic polyhedrosis virus. With this experience, we have identified a number of possible improvements in the suite of software specific to the icosahedral particle reconstruction in order to improve the ease of its future maintenance and upgrade, the accuracy of determined structure, the ease of usage by biology end-users and the computational efficiency. In this proposal, we will have four specific goals. The first aim is to rewrite the major codes in C++, which includes the icosahedral particle center and orientation refinement and the Fourier Bessel reconstruction. They will be optimized for both shared and distributed computer platforms and will be written in modular form to make them easy to maintain and modify. The second aim is to improve the algorithms for particle orientation parameter refinement, contrast transfer function and B factor corrections and Fourier Bessel reconstruction respectively. We expect that these improved codes will lead to a more accurate structure determination of icosahedral particles. The third aim is to integrate the improved codes with a Python language binder together with a user-friendly graphical interface and to output relevant intermediate data processing results that would allow the users to decide if the refinement is heading to the correct structure convergence. The fourth aim is to document the codes adequately with a help menu and to disseminate them broadly and freely through the internet access. Before the software release, we will confirm their reliability and accuracy by testing with simulated and experimental data. The experimental data consist of structures that we have previously determined to subnanometer resolution and for which the crystal structures of some of their components are known.

描述（由申请人提供）：许多球形病毒和某些酶复合物形成具有二十面体对称性的颗粒。电子冷冻显微镜和单个颗粒重建的使用使我们能够将这种类型的粒子的3维结构可视化到7-9 A分辨率。该分辨率足以解决长α螺旋并识别大型β床单。在过去的三年中，我们确定了6个二十体颗粒的结构，大小范围从该分辨率范围内的600 -1250 A不等。它们包括疱疹病毒衣壳，水稻矮人病毒，procapsid和p22噬菌体的成熟形式，轮状病毒和细胞质多角质 - 多面病毒。有了这一经验，我们已经确定了特定于二十面体粒子重建的软件套件的许多可能改进，以提高其未来维护和升级的便利性，确定结构的准确性，生物学最终用户使用的使用易于使用以及计算效率。在此提案中，我们将有四个具体的目标。第一个目的是重写C ++中的主要代码，其中包括二十面体粒子中心和方向改进以及傅立叶Bessel重建。它们将针对共享和分布式计算机平台进行优化，并以模块化形式编写，以使其易于维护和修改。第二个目的是改善粒子方向参数细化，对比度传递函数和B因子校正和傅立叶贝塞尔重建的算法。我们预计这些改进的代码将导致二十面体颗粒的更准确的结构测定。第三个目的是将改进的代码与Python语言活页夹与用户友好的图形接口集成在一起，并输出相关的中间数据处理结果，以使用户可以决定改进是否正向正确的结构收敛。第四个目的是通过帮助菜单充分记录代码，并通过互联网访问来广泛，自由地传播它们。在软件发布之前，我们将通过使用模拟和实验数据进行测试来确认它们的可靠性和准确性。实验数据由我们先前确定的结构组成，这些结构已确定为亚纳光分辨率，并已知其某些组件的晶体结构。