Core 4 - Computation Core

核心4-计算核心

基本信息

批准号：
10245112
负责人：
David A Case
金额：
$ 23.84万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-09-17 至 2023-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10245112
关键词：
Amber Area Base Sequence Bioinformatics Chemicals Communities Cryoelectron Microscopy Crystallography Data Development Elements Evolution Generations Genetic Variation HIV HIV Genome HIV-1 Lead Methods Molecular Conformation Publishing RNA RNA Sequences Research Personnel Roentgen Rays Sampling Sequence Analysis Services Software Framework Spectrum Analysis Structure Techniques Technology Technology Transfer Testing Untranslated RNA Viral Genome Visualization Work base computerized data processing experimental study molecular dynamics novel online resource programs reconstruction restraint simulation technology development tool

Amber Area Base Sequence Bioinformatics Chemicals Communities Cryoelectron Microscopy Crystallography Data Development Elements Evolution Generations Genetic Variation HIV HIV Genome HIV-1 Lead Methods Molecular Conformation Publishing RNA RNA Sequences Research Personnel Roentgen Rays Sampling Sequence Analysis Services Software Framework Spectrum Analysis Structure Techniques Technology Technology Transfer Testing Untranslated RNA Viral Genome Visualization Work base computerized data processing experimental study molecular dynamics novel online resource programs reconstruction restraint simulation technology development tool

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项目摘要

Core 4: Computation Summary The Computation Core provides both a service component (helping CRNA projects to make effective use of up-to-date tools in structure exploration, refinement, NMR analysis, and sequence analysis), and as a focus for technology development and technology transfer (especially in the areas of NMR structure determination, SAXS reconstructions, and sequence analysis). The technology development and transfer work focuses on three main areas: (i) using up-to-date molecular dynamics simulation methods and force fields to assist in structure determination based on crystallography, SAXS and cryo-EM data with a key emphasis on the development of novel ways to interpret small-angle X-ray scattering (SAXS) data and to combine this information with restraints derived from NMR, (ii) developing and supporting integrated tools for NMR spectrum analysis and structure generation and refinement with a key focus on creating novel tools to make use of chemical shifts in RNA structure analysis and refinement, and (iii) investigating the evolution of functional RNA sequences in the HIV-1 genome through analysis of nucleotide sequence data, which will lead to novel bioinformatics methods for identifying functional RNA elements in viral genomes, and the creation of a web resource to support these analyses for HIV-1.

核心4：计算概括计算核心既提供了服务组件（帮助CRNA项目有效利用结构探索，改进，NMR分析和序列分析中的最新工具），作为重点技术开发和技术转移（尤其是在NMR结构确定领域， SAXS重建和序列分析）。技术开发和转移工作的重点三个主要领域：（i）使用最新的分子动力学仿真方法和力场来协助基于晶体学，SAX和冷冻EM数据的结构确定，关键重点开发解释小角度X射线散射（SAXS）数据并结合起来的新型方法具有限制因素的信息，（ii）开发和支持NMR频谱的集成工具分析和结构生成和完善，关注创建新颖的工具以利用 RNA结构分析和改进的化学位移，以及（iii）研究功能RNA的演变通过分析核苷酸序列数据，HIV-1基因组中的序列将导致新颖用于识别病毒基因组中功能性RNA元素的生物信息学方法，并创建Web 支持HIV-1分析的资源。