Metal binding sites in macromolecular structures
Metal binding sites in macromolecular structures
批准号:
9008644
负责人:
WLADEK MINOR
金额:
$34.31万
依托单位:
依托单位国家:
美国
项目类别:
财政年份:
2016
资助国家:
美国
项目状态:
已结题
起止时间:
2016-03-01 至 2019-11-30
关键词:
AlgorithmsArchitectureAreaBindingBinding SitesBiochemical ReactionBiologicalBiological ProcessBiomedical ResearchBiophysical ProcessCatalogingCatalogsCatalysisChemicalsClassificationCollectionCommunitiesComplementCustomDNADataData SetDatabasesDepositionDetectionDevelopmentDiagnosticElectron TransportElementsEnvironmentFutureGasesGuidelinesHeavy MetalsInternetInvestigationIonsIronKnowledgeLifeMachine LearningMagnesiumManualsMapsMetal Binding SiteMetal Ion BindingMetalsMethodologyMiningModelingMolecular StructureNamesNucleic AcidsNucleotidesOnline SystemsPlayPolyphosphatesProceduresProductionPropertyProteinsRNAResearchResearch PersonnelResourcesRetrievalRoleSiteStructural BiologistStructureSurveysSystemTherapeuticTo specifyTrainingUpdateValidationVariantWorkZincabstractingbasecomparativecomputerized toolsdatabase structuredensitydesigndrug discoveryelectron densityexperienceinfancyinterestmacromoleculemodel buildingprotein foldingprotein structure predictionsupport toolstool
中文摘要
项目:大分子结构中的金属结合环境
翻译后摘要:金属离子在生物大分子的机制和结构中起着至关重要的作用,
包括生物化学反应的催化、电子传递、气体的结合和
核苷酸和其它多磷酸盐化合物。然而,最近一项对公共结构的调查显示,
沉积在PDB中的含金属蛋白质和核酸揭示了大量的错误鉴定的
和/或次优建模的金属结合位点。这促使创建了一个诊断工具
金属结合微环境模型,“CheckMyMetal”(CMM)网络服务器
(http://csgid.org/csgid/metal_sites/),该软件可检测金属结构中的几何形状和其他不规则性
结合位点,并提醒研究人员在金属分配的潜在错误。作为CMM的生产版本,
已经获得了广泛的使用,研究界已经确定了未来发展的几个方向
主要兴趣:1)研究和验证大分子中不常见的重金属结合位点
结构; 2)建立服务器以提供高质量、经验证的金属结合位点的定制子集; 3)
开发工具,自动检测电子密度中可能的金属结合位点,并识别和添加
在晶体学模型建立和改进过程中最可几金属离子; 4)系统地编目
金属结合结构并检测新的金属结合基序。我们建议开发的工具包,
CMM作为一个基础,包含几个模块,这些模块可以独立工作,也可以作为
结构建模、验证、解释和注释流水线。这项提案不仅是为了
结构生物学家在晶体学模型构建过程中建模和验证新结构,
改进,而且也为更广泛的观众-生物医学研究人员研究含金属的蛋白质和
核酸
英文摘要
Project: Metal binding environments in macromolecular structures
Abstract: Metal ions play vital roles in both the mechanism and architecture of biological macromolecules,
including the catalysis of biochemical reactions, electron transport, binding of gases, and stabilization of
nucleotides and other polyphosphate compounds. However, a recent survey of publicly available structures of
metal-containing proteins and nucleic acids deposited in the PDB revealed an abundance of misidentified
and/or sub-optimally modeled metal binding sites. This prompted the creation of a diagnostic tool for the
models of metal binding microenvironments, the "CheckMyMetal" (CMM) web server
(http://csgid.org/csgid/metal_sites/), which detects geometric and other irregularities in structures of metal
binding sites and alerts researchers to potential errors in metal assignment. As the production version of CMM
has gained widespread usage, the research community has identified several directions for future development
of major interest:1) investigate and validate uncommon heavy metal binding sites in macromolecular
structures; 2) establish a server to provide customized subsets of high-quality, validated metal binding sites; 3)
develop tools to automatically detect likely metal binding sites in electron density, and identify and add the
most probable metal ion during crystallographic model building and refinement; and 4) systematically catalog
metal binding architectures and detect new metal binding motifs. The toolkit we propose to develop, using
CMM as a basis, contains several modules that will work either independently or as integrated steps in the
structure modeling, validation, interpretation and annotation pipeline. This proposal was designed not only for
structural biologists to model and validate new structures during crystallographic model building and
refinement, but also for a broader audience—biomedical researchers studying metal-containing proteins and
nucleic acids.
期刊论文(0)
专著(0)
科研奖励(0)
会议论文
Reproducible, Unbiased Ligand Identification Assisted by Artificial Intelligence and Development of Ligand Reference Libraries
-
批准号:10019572
-
项目类别:
-
资助金额:$56.12万
-
财政年份:2019
-
负责人:WLADEK MINOR
-
依托单位:
Reproducible, Unbiased Ligand Identification Assisted by Artificial Intelligence and Development of Ligand Reference Libraries
-
批准号:10432049
-
项目类别:
-
资助金额:$56.12万
-
财政年份:2019
-
负责人:WLADEK MINOR
-
依托单位:
Reproducible, Unbiased Ligand Identification Assisted by Artificial Intelligence and Development of Ligand Reference Libraries
-
批准号:10200091
-
项目类别:
-
资助金额:$56.12万
-
财政年份:2019
-
负责人:WLADEK MINOR
-
依托单位:
Metal binding sites in macromolecular structures
-
批准号:9233159
-
项目类别:
-
资助金额:$32.91万
-
财政年份:2016
-
负责人:WLADEK MINOR
-
依托单位:
Integrated resource for reproducibility in macromolecular crystallography
-
批准号:9280987
-
项目类别:
-
资助金额:$47.19万
-
财政年份:2015
-
负责人:WLADEK MINOR
-
依托单位:
X-ray data analysis in the presence of structural variability
-
批准号:9147618
-
项目类别:
-
资助金额:$33.52万
-
财政年份:2015
-
负责人:WLADEK MINOR
-
依托单位:
Integrated resource for reproducibility in macromolecular crystallography
-
批准号:8875830
-
项目类别:
-
资助金额:$46.0万
-
财政年份:2015
-
负责人:WLADEK MINOR
-
依托单位:
X-ray data analysis in the presence of structural variability
-
批准号:9552204
-
项目类别:
-
资助金额:$33.52万
-
财政年份:2015
-
负责人:WLADEK MINOR
-
依托单位:
Integrated resource for reproducibility in macromolecular crystallography
-
批准号:9069902
-
项目类别:
-
资助金额:$47.19万
-
财政年份:2015
-
负责人:WLADEK MINOR
-
依托单位:
Centers for High-Throughput Structure Determination
-
批准号:8152878
-
项目类别:
-
资助金额:$30.37万
-
财政年份:2010
-
负责人:WLADEK MINOR
-
依托单位:
The Protein Structure Initiative Knowledgebase
-
批准号:8152401
-
项目类别:
-
资助金额:$10.1万
-
财政年份:2010
-
负责人:WLADEK MINOR
-
依托单位:
Subproject #6
-
批准号:7099071
-
项目类别:
-
资助金额:$48.67万
-
财政年份:2005
-
负责人:WLADEK MINOR
-
依托单位:
The Crystallography of Macromolecules
-
批准号:8657051
-
项目类别:
-
资助金额:$32.01万
-
财政年份:1996
-
负责人:WLADEK MINOR
-
依托单位:
The Crystallography of Macromolecules
-
批准号:8108523
-
项目类别:
-
资助金额:$34.19万
-
财政年份:1996
-
负责人:WLADEK MINOR
-
依托单位:
The Crystallography of Macromolecules
-
批准号:8269876
-
项目类别:
-
资助金额:$32.33万
-
财政年份:1996
-
负责人:WLADEK MINOR
-
依托单位:
The Crystallography of Macromolecules
-
批准号:8470172
-
项目类别:
-
资助金额:$30.91万
-
财政年份:1996
-
负责人:WLADEK MINOR
-
依托单位:
Subproject #6
-
批准号:7312244
-
项目类别:
-
资助金额:$50.95万
-
财政年份:--
-
负责人:WLADEK MINOR
-
依托单位:
The Protein Structure Initiative Knowledgebase
-
批准号:8692858
-
项目类别:
-
资助金额:$9.46万
-
财政年份:--
-
负责人:WLADEK MINOR
-
依托单位:
Subproject #6
-
批准号:7457675
-
项目类别:
-
资助金额:$76.29万
-
财政年份:--
-
负责人:WLADEK MINOR
-
依托单位:
Subproject #6
-
批准号:7656726
-
项目类别:
-
资助金额:$77.15万
-
财政年份:--
-
负责人:WLADEK MINOR
-
依托单位:
海外基金