ITR: Subnanometer Structure Based Fold Determination of Biological Complex

美国德克萨斯大学洛杉矶分校Bajaj合作伙伴： ITR：基于亚纳米结构的生物复合物折叠测定。我们建议组建一个由三名具有不同专业知识的独立研究人员组成的团队，共同开发必要的计算和可视化方法，以便生物学家快速，轻松，准确地推断大分子复合物结构域组分的折叠。虽然大分子复合物的结构变得越来越普遍，一些密度图的大小将增加到1GB，但提取重要生物信息的可视化和分析要求远远超出了目前可用的软件。我们的研究任务将探索不同的算法来增强信号通过去噪的三维结构，有效地可视化这些大的和过滤的地图，提取单个蛋白质组分及其显着的结构特征，如a螺旋和B片准确，并最终构建伪原子模型与新的结构预测方法，蛋白质序列和结构的考虑作为约束。我们将建立一个测试数据集，包括模拟和实验结构，以验证我们的每个开发步骤。每个研究中心的软件开发将使用脚本语言（Python）粘合在一起，并通过图形界面易于使用。此外，该软件将通过开放源码政策进行广泛记录和分发，鼓励继续合作和开发。

EIA-0325550 University of Texas Chandrajit L. Bajaj COLLABORATIVES: ITR: Subnanometer Structure Based Fold Determination of Biological Complexes . We propose to form a team of three independent investigators with different expertises to co-develop the necessary computation and visualization methodology for biologists to quickly, easily and accurately deduce the folds of the domain components of large macromolecular complexes. While structures of macromolecular complexes are becoming more prevalent, and the size of some density maps would increase up to 1GB, the visualization and analysis requirements to extract important biological information are far beyond the currently available software. Our research task will explore different algorithms to enhance the signal through denoising of the 3-dimensional structure, visualize these large and filtered maps effectively, extract the individual protein components and their salient structural features such as a helices and b sheets accurately, and ultimately construct pseudo atomic model with novel structure prediction methods using protein sequence and structure considerations as constraints. We will set up a test data set, comprised of both simulated and experimental structures, to validate each of our development steps. The software developments in each of the research sites will be glued together using a scripting language (Python) and made easy to use through a graphical interface. Additionally, the software will be extensively documented and distributed via an open source policy, encouraging continued collaboration and development.