CHIMERA EXTENSIONS FOR IMP
IMP 的嵌合体延伸
基本信息
- 批准号:8363631
- 负责人:
- 金额:$ 2.79万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2011
- 资助国家:美国
- 起止时间:2011-07-01 至 2012-06-30
- 项目状态:已结题
- 来源:
- 关键词:AlgorithmsAreaChimera organismCryoelectron MicroscopyDataFeedbackFundingGrantGraphImageryIndividualInformaticsManualsMapsModelingModificationNational Center for Research ResourcesPositioning AttributePrincipal InvestigatorProcessProteinsProteomicsRelative (related person)ResearchResearch InfrastructureResourcesRoentgen RaysRunningSourceStructureTorsionUnited States National Institutes of Healthbiocomputingcomparativecostdensityprocess optimizationprogramsprotein complexrestraintthree dimensional structureweb services
项目摘要
This subproject is one of many research subprojects utilizing the resources
provided by a Center grant funded by NIH/NCRR. Primary support for the subproject
and the subproject's principal investigator may have been provided by other sources,
including other NIH sources. The Total Cost listed for the subproject likely
represents the estimated amount of Center infrastructure utilized by the subproject,
not direct funding provided by the NCRR grant to the subproject or subproject staff.
In conjunction with Prof. Andrej Sali's group at UCSF, we will implement Chimera extensions and web services to support protein and protein complex modeling in three main areas:
1) Comparative modeling and loop modeling of individual proteins.
Specifically, we will take the algorithms implemented as part of the widely used
comparative modeling program Modeller, and make them available as a web service. We will then enhance Chimera so that a user providing a sequence to be modeled and a structure to be used as the template could use this web service to produce a model.
2) Determination of the structures of large assemblies using cryoEM and proteomics data.
We will use Chimera to view and guide the process of determining the structures of large assemblies with IMP using cryoEM and proteomics data. The user will be able to view and refine models at intermediate steps of the optimization process. Chimera will be used to display the density map and an anchor graph, which shows the approximate positions of protein centroids in the assembly and the interactions among them. The anchor graph is calculated by the MultiFit. We will support the following ways of interacting with the MultiFit process: 1) manual positioning and orientating of the proteins in the density guided by the anchor graph and then calling MultiFit for local refinement; 2) manual positioning of proteins on anchor points but using MultiFit to search all possible orientations; 3) manual positioning and orientating of proteins within the assembly model guided by dynamic feedback of the individual restraint values and overall score from MultiFit; and 4) running MultiFit without any initial positioning but allowing manual refinement at intermediate steps as described above.
3) Structural refinement and fitting using Small Angle X-Ray Scattering (SAXS) data.
We will support the use of experimental and computed SAXS profiles to guide the modification and refinement of modeled structures. The following ways of combining 3D structure and SAXS profiles will be implemented: 1) loading a structure and SAXS profile simultaneously and displaying them together; 2) computing and displaying the SAXS profile for part or all of the displayed structure; 3) fitting the computational SAXS profile to the experimental one and displaying them together; 4) recalculating the SAXS profile
automatically as the structure is interactively modified (for example, by changing torsion angles or moving proteins relative to each other); and 5) refining the assembly model to better fit the experimental SAXS profile
using an IMP web service.
这个子项目是利用资源的许多研究子项目之一。
由NIH/NCRR资助的中心拨款提供。对子项目的主要支持
子项目的首席调查员可能是由其他来源提供的,
包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能
表示该子项目使用的中心基础设施的估计数量,
不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。
与加州大学旧金山分校的Andrej Sali教授的团队合作,我们将实施嵌合体扩展和Web服务,以支持三个主要领域的蛋白质和蛋白质复合体建模:
1)单个蛋白质的比较建模和环路建模。
具体地说,我们将把实现的算法作为广泛使用的
比较建模程序Modeler,并将其作为Web服务提供。然后,我们将增强Chimera,以便提供要建模的序列和要用作模板的结构的用户可以使用此Web服务来生成模型。
2)使用低温电子显微镜和蛋白质组学数据确定大组件的结构。
我们将使用嵌合体来查看和指导使用低温EM和蛋白质组学数据确定IMP大型组件结构的过程。用户将能够在优化过程的中间步骤查看和改进模型。嵌合体将被用来显示密度图和锚图,该图显示了蛋白质质心在组装中的大致位置以及它们之间的相互作用。锚点图形由MultiFit计算。我们将支持以下与MultiFit过程交互的方式:1)在锚图引导的密度中手动定位和定向蛋白质,然后调用MultiFit进行局部细化;2)在锚点上手动定位蛋白质,但使用MultiFit搜索所有可能的定向;3)在组装模型中手动定位和定向蛋白质,由来自MultiFit的个体约束值和总得分的动态反馈指导;以及4)运行MultiFit而不需要任何初始定位,但允许如上所述在中间步骤进行手动细化。
3)利用小角X射线散射(SAXS)数据进行结构细化和拟合。
我们将支持使用实验和计算的SAXS轮廓来指导对建模结构的修改和改进。实现了将三维结构和SAXS剖面相结合的方法:1)同时加载结构和SAXS剖面并将它们一起显示;2)计算和显示部分或全部显示的结构的SAXS剖面;3)将计算的SAXS剖面与实验的SAXS剖面进行拟合并一起显示;4)重新计算SAXS剖面
当结构被交互修改时自动地(例如,通过改变扭转角度或相互移动蛋白质);以及5)改进组装模型以更好地匹配实验SAXS轮廓
使用IMP Web服务。
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)
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{{ truncateString('THOMAS E FERRIN', 18)}}的其他基金
ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling
ChimeraX——用于多尺度建模的下一代可视化和分析软件
- 批准号:
10707058 - 财政年份:2018
- 资助金额:
$ 2.79万 - 项目类别:
ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling
ChimeraX——用于多尺度建模的下一代可视化和分析软件
- 批准号:
10442109 - 财政年份:2018
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ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling
ChimeraX——用于多尺度建模的下一代可视化和分析软件
- 批准号:
10192752 - 财政年份:2018
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ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling
ChimeraX——用于多尺度建模的下一代可视化和分析软件
- 批准号:
9973164 - 财政年份:2018
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ENHANCE CHIMERA'S ANIMATION AND PHYSICAL MODELING CAPABILITIES
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8363632 - 财政年份:2011
- 资助金额:
$ 2.79万 - 项目类别:
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