Computation and Data Science

计算和数据科学

• 批准号: 10221477
• 负责人: Nels C. Elde
• 金额: $ 32.71万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-27 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10221477
• 关键词: Bacteriophages; Binding; Biochemical; Biological Process; Biology; Cellular biology; Communication; Communication Research; Complementary DNA; Computational Science; Computer Models; Couples; Data; Data Science; Data Science Core; Elements; Evolution; Genes; Genomics; Grain; HIV; Human Biology; Immune; Letters; Libraries; Life Cycle Stages; Ligand Binding; Lighting; Modeling; Molecular; Molecular Biology; Peptides; Phylogenetic Analysis; Primates; Process; Property; Protein Engineering; Proteins; Resources; Solubility; Structure; Variant; Yeasts; animation; design; experimental study; flexibility; genome-wide; high throughput screening; models and simulation; molecular dynamics; outreach; screening; structural biology; three-dimensional visualization; trafficking

ABSTRACT The Computation and Data Science Core provides a variety of computational capabilities that will support and enhance discovery and illumination of HIV biology. We have created a flexible and robust protein engineering platform that couples both design and screening approaches).1-10 These capabilities support de novo protein design and optimization of ligand binding, assembly, stability, and solubility properties. Complementary resources enable high-throughput screening using phage and yeast display.11 Computational modeling is further bolstered by atomistic and coarse-grained molecular dynamics simulations that leverage experimental datasets12,13 and multiscale parameterization strategies14-23 to model different interactions in the HIV life cycle and generate testable hypotheses. Conceptual depth is added by a range of evolutionary genomics resources, including phylogenetic and discovery pipelines that draw on primate diversity to inform human biology and provide access to primate gene sequences and cDNA clones to extend our biochemical and structural studies.24-27 Finally, we have established unique capabilities in molecular animation, scientific communication, and public outreach that feature the creation and dissemination of sophisticated, dynamic 3D visualizations of biological processes.

抽象的 计算和数据科学核心提供了各种计算能力，支持和 加强艾滋病毒生物学的发现和阐明。我们创建了灵活且强大的蛋白质工程 结合设计和筛选方法的平台）。1-10 这些功能支持 de novo 蛋白质 配体结合、组装、稳定性和溶解度特性的设计和优化。补充 资源可以使用噬菌体和酵母展示进行高通量筛选。11 计算模型是 利用实验的原子和粗粒度分子动力学模拟进一步支持 数据集12,13和多尺度参数化策略14-23来模拟艾滋病毒生命周期中的不同相互作用 并产生可检验的假设。一系列进化基因组学资源增加了概念深度， 包括利用灵长类动物多样性为人类生物学提供信息的系统发育和发现管道 提供灵长类基因序列和 cDNA 克隆，以扩展我们的生化和结构 研究。24-27 最后，我们在分子动画、科学传播、 以及公共宣传，其特点是创建和传播复杂的动态 3D 可视化 生物过程。