Extending MolProbity Diagnosis & Healing Methods to Empower Better CryoEM & Xray Models at 2.5-4A Resolution, plus Versioned, Redeposited "GEMS" for Important Individual Structures
扩展 MolProbity 诊断
基本信息
- 批准号:10166392
- 负责人:
- 金额:$ 24.15万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2019
- 资助国家:美国
- 起止时间:2019-06-01 至 2024-05-31
- 项目状态:已结题
- 来源:
- 关键词:20 year old3-DimensionalAddressBiologyCodeCommunicationCommunitiesComputer softwareContractorCoupledCryoelectron MicroscopyCrystallographyDataDepositionDiagnosisDrug DesignFutureGoalsHandHydrogenHydrogen BondingIndividualInternetInvestmentsLaboratoriesLanguageLibrariesMaintenanceMeasuresMemoryMethodsModelingModernizationMolecular MachinesNucleic AcidsOccupationsPlayProcessProteinsPythonsRNAReadingReportingResearch Project GrantsResolutionRiboseRoentgen RaysRoleSecureSecurityServicesSoftware ToolsSoftware ValidationStandardizationStructural BiologistStructureSystemTestingTimeUpdateVaccinesValidationVertebral columnWorkWritingbaseconformerdata structuredata warehousedesignexperiencehealingimprovedinterestinteroperabilitymacromoleculemodel buildingopen sourceprogramssoftware systemsstructural biologystructured datathree-dimensional modelingvirtual machineweb services
项目摘要
Summary/Abstract for Supplement
MolProbity macromolecular model validation assigns overall quality scores, but most importantly, it reports
probable local errors with graphic flags that help structural biologists fix most of those errors. It is
considered state-of-the-art for model validation, has a large worldwide user base, is incorporated into most
model-building and refinement software systems, and is central to model validation at the Protein DataBank.
The component programs add and optimize hydrogen atoms to analyze and display all-atom contacts (H-
bonds, favorable van der Waals, and serious steric "clashes" of unfavorable overlaps ≥0.4Å). That
distinctive feature of MolProbity is augmented with updated versions of traditional validation measures such
as Ramachandran and rotamers, with RNA ribose pucker and backbone conformers, and most recently with
new criteria such as CaBLAM that are especially useful at the 2.5-4Å resolutions common for structures of
exciting "molecular machines" obtained by crystallography or cryoEM.
The programs in this effective and widely used toolset are diverse and rather loosely coupled, and some are
more than 20 years old. For quite a while they have been in great need of a deep rewrite and modernization
beyond what an academic research grant can support, in order to stay maintainable, extensible, and robust.
Our problem with the MolProbity code is the sort of dilemma that this new type of supplement is designed to
solve, in order to provide open scientific software that enables its users to take full advantage of the broad
capabilities now possible for secure and stable accessibility, interoperability, and re-use.We believe
MolProbity is worth this investment, first to the structural biology community and second to the biomedical
end-users of these structures.
I am very fortunate to have identified a professional contractor highly experienced in many challenging
computational improvements, rewrites, and interactive 3D graphics, that is somewhat familiar with
macromolecules and interested in taking on this project. The current plan is to unify our MolProbity code
base around Python with calls to well-optimized and hardened libraries in C++ or C, and to use the same
standard-format parsers, internal data hierarchy, in-memory communication, and open CCTBX toolbox
utilities used by the most recent of our programs which are integrated with the Phenix software system. The
rewrite will include more complete regression tests, develop a standardized build process, and explore a
variety of cloud hosting options for the web service.
摘要/补充摘要
MolProbity大分子模型验证分配整体质量分数,但最重要的是,它报告
可能的局部错误,并带有图形标记,帮助结构生物学家修复大部分错误。是
被认为是最先进的模型验证,拥有庞大的全球用户群,被纳入大多数
模型构建和优化软件系统,是蛋白质数据库模型验证的核心。
组件程序添加和优化氢原子,以分析和显示所有原子接触(H-
键,有利的货车德瓦耳斯,和严重的空间“冲突”的不利重叠≥ 0.4倍)。的
MolProbity的独特功能通过传统验证措施的更新版本得到增强,
作为Ramachandran和旋转异构体,与RNA核糖折叠和骨架构象异构体,最近与
新的标准,如CaBLAM,特别适用于2.5- 4 μ m分辨率的结构,
令人兴奋的“分子机器”通过晶体学或cryoEM获得。
这个有效且广泛使用的工具集中的程序是多样的,而且耦合相当松散,
20多岁了很长一段时间以来,他们一直非常需要深刻的重写和现代化
超出了学术研究资助所能支持的范围,以保持可维护性、可扩展性和健壮性。
我们对MolProbity代码的问题是这种新型补充的设计目的是为了
解决,以提供开放的科学软件,使其用户能够充分利用广泛的
现在,安全稳定的可访问性、互操作性和重复使用功能成为可能。我们相信,
MolProbity值得这笔投资,首先是对于结构生物学界,其次是对于生物医学界
这些结构的最终用户。
我很幸运能找到一个专业的承包商,在许多具有挑战性的
计算改进,重写和交互式3D图形,这是有点熟悉
大分子,并有兴趣承担这个项目。目前的计划是统一我们的MolProbity代码
基于Python,调用C++或C中优化和强化的库,并使用相同的
标准格式解析器、内部数据层次结构、内存通信和开放式CCTBX工具箱
我们最新的程序所使用的实用程序,这些程序与Phenix软件系统集成。的
重写将包括更完整的回归测试,开发标准化的构建过程,并探索
为网络服务提供各种云托管选项。
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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DAVID Claude RICHARDSON其他文献
DAVID Claude RICHARDSON的其他文献
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{{ truncateString('DAVID Claude RICHARDSON', 18)}}的其他基金
Extending MolProbity Diagnosis & Healing Methods to Empower Better CryoEM & Xray Models at 2.5-4A Resolution, plus Versioned, Redeposited "GEMS" for Important Individual Structures
扩展 MolProbity 诊断
- 批准号:
10170382 - 财政年份:2019
- 资助金额:
$ 24.15万 - 项目类别:
Extending MolProbity Diagnosis & Healing Methods to Empower Better CryoEM & Xray Models at 2.5-4A Resolution, plus Versioned, Redeposited "GEMS" for Important Individual Structures
扩展 MolProbity 诊断
- 批准号:
10414895 - 财政年份:2019
- 资助金额:
$ 24.15万 - 项目类别:
New Kind of Quality Management for X-ray and NMR Models
X 射线和 NMR 模型的新型质量管理
- 批准号:
7921709 - 财政年份:2009
- 资助金额:
$ 24.15万 - 项目类别:
MolProbity Service and Related 3D-Analysis Resources
MolProbity 服务和相关 3D 分析资源
- 批准号:
7069249 - 财政年份:2006
- 资助金额:
$ 24.15万 - 项目类别:
MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine
摩尔概率验证
- 批准号:
9339700 - 财政年份:2006
- 资助金额:
$ 24.15万 - 项目类别:
MolProbity Service and Related 3D-Analysis Resources
MolProbity 服务和相关 3D 分析资源
- 批准号:
7254966 - 财政年份:2006
- 资助金额:
$ 24.15万 - 项目类别:
MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine
摩尔概率验证
- 批准号:
8242090 - 财政年份:2006
- 资助金额:
$ 24.15万 - 项目类别:
MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine
摩尔概率验证
- 批准号:
8077177 - 财政年份:2006
- 资助金额:
$ 24.15万 - 项目类别:
MolProbity Service and Related 3D-Analysis Resources
MolProbity 服务和相关 3D 分析资源
- 批准号:
7458635 - 财政年份:2006
- 资助金额:
$ 24.15万 - 项目类别:
MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine
摩尔概率验证
- 批准号:
8475482 - 财政年份:2006
- 资助金额:
$ 24.15万 - 项目类别:
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