Core 4 Sali Echeverria
核心 4 萨利·埃切维里亚
基本信息
- 批准号:10506986
- 负责人:
- 金额:$ 21.37万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2022
- 资助国家:美国
- 起止时间:2022-07-15 至 2027-04-30
- 项目状态:未结题
- 来源:
- 关键词:Affinity ChromatographyAlgorithmsArchitectureBiochemicalBioinformaticsBiologyCD4 Positive T LymphocytesCRISPR/Cas technologyComplexComputer softwareCryoelectron MicroscopyDataData AnalysesData SetDeuteriumDevelopmentGeneticGenetic TranscriptionGoalsHIVHIV InfectionsHIV-1HeterogeneityHumanHydrogenIndividualIntegration Host FactorsLabelLeadMapsMass Spectrum AnalysisMethodsModelingMolecular ConformationPathway interactionsPeptidesPost-Translational Protein ProcessingProteinsProteomicsResolutionServicesStatistical Data InterpretationStructural ModelsStructureSystems BiologyViralVisualizationbasecell typecrosslinkdata integrationdata toolsdensityflexibilitygenome editinggenome-wide analysisimprovedmultiple data typesmutation screeningnetwork modelsopen sourceparticlepathogenprotein complexprotein protein interactionrestraintstructural biologysuccesstool
项目摘要
THE HARC CENTER: HIV ACCESSORY AND REGULATORY COMPLEXES
COMPUTATIONAL CORE
SUMMARY
The overall goal of the Computational Core is to facilitate the analysis and interpretation of multiple data types
across Projects and Cores to characterize the cellular networks, proteins, and protein complexes that influence
HIV replication and latency. We will employ existing bioinformatics and systems biology approaches, as well as
develop new methods to facilitate the unification of mechanistic and structural details with network biology, with
a strong emphasis on the analysis and integration of data derived from proteomics, genetics, and structural
biology approaches. Specifically, we will provide the tools to identify interactions of endogenous proviral and
antiviral HIV-host protein complexes that have been structurally and functionally characterized by the
Proteomics, Genetics, and Structural Biology Cores. This includes datasets from affinity purification mass
spectrometry (AP-MS), native mass spectrometry (nMS), cross-linking mass spectrometry (XL-MS),
hydrogen/deuterium exchange mass spectrometry (H/DX-MS), systematic genome editing by CRISPR-Cas9,
deep mutational scanning (DMS), and cryo-electron microscopy (cryo-EM). These datasets will be analyzed
separately as well as jointly, followed by visualization to gain a deeper understanding of the functional pathways
that are modulated during HIV infection. Finally, we will determine the structures of HIV-human protein
complexes by an integrative approach using various proteomics, genetics, structural, and biochemical data.
Integrative structure determination will be performed using the open-source Integrative Modeling Platform (IMP)
package developed in the Sali lab (Core Lead). We will initially focus on protein complexes containing human or
simian A3Gs, and HIV-1 Vif, Rev, and Tat, followed by structure determination of HIV-human complexes
identified from CD4+ T cells and structurally interrogated by the Proteomics Core.
HARC中心:艾滋病毒附件和调节复合物
计算核心
总结
计算核心的总体目标是促进多种数据类型的分析和解释
跨项目和核心,以表征细胞网络,蛋白质和蛋白质复合物,
HIV复制和潜伏期。我们将采用现有的生物信息学和系统生物学方法,以及
开发新的方法,以促进统一的机制和结构细节与网络生物学,
非常重视分析和整合来自蛋白质组学,遗传学和结构的数据
生物学方法。具体来说,我们将提供工具,以确定内源性前病毒的相互作用,
抗病毒HIV-宿主蛋白复合物的结构和功能特征在于:
蛋白质组学、遗传学和结构生物学核心。这包括来自亲和纯化质量的数据集
质谱法(AP-MS),天然质谱法(nMS),交联质谱法(XL-MS),
氢/氘交换质谱(H/DX-MS),通过CRISPR-Cas9进行的系统性基因组编辑,
深突变扫描(DMS)和冷冻电子显微镜(cryo-EM)。将对这些数据集进行分析
分别以及联合,然后可视化,以获得更深入的了解功能途径
在HIV感染过程中被调节。最后,我们将确定HIV-人蛋白的结构
复合物的综合方法使用各种蛋白质组学,遗传学,结构和生化数据。
将使用开源集成建模平台(IMP)进行集成结构确定
Sali实验室开发的软件包(核心负责人)。我们将首先集中在蛋白质复合物含有人类或
猴A3 Gs和HIV-1 Vif、Rev和达特,然后测定HIV-人复合物的结构
从CD 4 + T细胞中鉴定并通过蛋白质组学核心进行结构分析。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
数据更新时间:{{ journalArticles.updateTime }}
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
ANDREJ SALI其他文献
ANDREJ SALI的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
{{ truncateString('ANDREJ SALI', 18)}}的其他基金
CORE 1: Data Management and Bioinformatics Core
核心 1:数据管理和生物信息学核心
- 批准号:
10549998 - 财政年份:2018
- 资助金额:
$ 21.37万 - 项目类别:
TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular Neighborhoods
TR
- 批准号:
10401763 - 财政年份:2014
- 资助金额:
$ 21.37万 - 项目类别:
TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular Neighborhoods
TR
- 批准号:
10621361 - 财政年份:2014
- 资助金额:
$ 21.37万 - 项目类别:
DEVELOPMENT AND TESTING OF MODELLER, AND RELATED TOOLS, ON THE ALPHA PLATFORM
在 ALPHA 平台上开发和测试 MODELER 及相关工具
- 批准号:
8363599 - 财政年份:2011
- 资助金额:
$ 21.37万 - 项目类别:
DETERMINATION OF THE PSEUDO-ATOMIC STRUCTURE OF NUCLEAR PORE COMPLEX (NPC) COMPO
核孔复合体(NPC)复合物拟原子结构的测定
- 批准号:
8362329 - 财政年份:2011
- 资助金额:
$ 21.37万 - 项目类别:
COMPUTATIONAL MODELING OF THE STRUCTURE OF THE SPINDLE POLE BODY CORE
主轴极体铁芯结构的计算模型
- 批准号:
8365787 - 财政年份:2011
- 资助金额:
$ 21.37万 - 项目类别:
相似海外基金
CAREER: Efficient Algorithms for Modern Computer Architecture
职业:现代计算机架构的高效算法
- 批准号:
2339310 - 财政年份:2024
- 资助金额:
$ 21.37万 - 项目类别:
Continuing Grant
Collaborative Research: SHF: Small: Artificial Intelligence of Things (AIoT): Theory, Architecture, and Algorithms
合作研究:SHF:小型:物联网人工智能 (AIoT):理论、架构和算法
- 批准号:
2221742 - 财政年份:2022
- 资助金额:
$ 21.37万 - 项目类别:
Standard Grant
Collaborative Research: SHF: Small: Artificial Intelligence of Things (AIoT): Theory, Architecture, and Algorithms
合作研究:SHF:小型:物联网人工智能 (AIoT):理论、架构和算法
- 批准号:
2221741 - 财政年份:2022
- 资助金额:
$ 21.37万 - 项目类别:
Standard Grant
Algorithms and Architecture for Super Terabit Flexible Multicarrier Coherent Optical Transmission
超太比特灵活多载波相干光传输的算法和架构
- 批准号:
533529-2018 - 财政年份:2020
- 资助金额:
$ 21.37万 - 项目类别:
Collaborative Research and Development Grants
OAC Core: Small: Architecture and Network-aware Partitioning Algorithms for Scalable PDE Solvers
OAC 核心:小型:可扩展 PDE 求解器的架构和网络感知分区算法
- 批准号:
2008772 - 财政年份:2020
- 资助金额:
$ 21.37万 - 项目类别:
Standard Grant
Algorithms and Architecture for Super Terabit Flexible Multicarrier Coherent Optical Transmission
超太比特灵活多载波相干光传输的算法和架构
- 批准号:
533529-2018 - 财政年份:2019
- 资助金额:
$ 21.37万 - 项目类别:
Collaborative Research and Development Grants
Visualization of FPGA CAD Algorithms and Target Architecture
FPGA CAD 算法和目标架构的可视化
- 批准号:
541812-2019 - 财政年份:2019
- 资助金额:
$ 21.37万 - 项目类别:
University Undergraduate Student Research Awards
Collaborative Research: ABI Innovation: Algorithms for recovering root architecture from 3D imaging
合作研究:ABI 创新:从 3D 成像恢复根结构的算法
- 批准号:
1759836 - 财政年份:2018
- 资助金额:
$ 21.37万 - 项目类别:
Standard Grant
Collaborative Research: ABI Innovation: Algorithms for recovering root architecture from 3D imaging
合作研究:ABI 创新:从 3D 成像恢复根结构的算法
- 批准号:
1759796 - 财政年份:2018
- 资助金额:
$ 21.37万 - 项目类别:
Standard Grant
Collaborative Research: ABI Innovation: Algorithms for recovering root architecture from 3D imaging
合作研究:ABI 创新:从 3D 成像恢复根结构的算法
- 批准号:
1759807 - 财政年份:2018
- 资助金额:
$ 21.37万 - 项目类别:
Standard Grant