用于蛋白质组学和结构数据交互探索的计算工具。
Computational tools for the interactive exploration of proteomic and structural data.
机构信息
Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA.
出版信息
Mol Cell Proteomics. 2010 Aug;9(8):1703-15. doi: 10.1074/mcp.R000007-MCP201. Epub 2010 Jun 4.
Abstract
Linking proteomics and structural data is critical to our understanding of cellular processes, and interactive exploration of these complementary data sets can be extremely valuable for developing or confirming hypotheses in silico. However, few computational tools facilitate linking these types of data interactively. In addition, the tools that do exist are neither well understood nor widely used by the proteomics or structural biology communities. We briefly describe several relevant tools, and then, using three scenarios, we present in depth two tools for the integrated exploration of proteomics and structural data.
摘要
将蛋白质组学和结构数据联系起来对于我们理解细胞过程至关重要，交互式探索这些互补数据集对于在计算机上开发或验证假设非常有价值。然而，很少有计算工具能够方便地进行这种类型的数据交互链接。此外，现有的工具既没有被很好地理解，也没有被蛋白质组学或结构生物学领域广泛使用。我们简要描述了几个相关的工具，然后，通过三个场景，深入介绍了两种用于蛋白质组学和结构数据集成探索的工具。
相似文献
1
Computational tools for the interactive exploration of proteomic and structural data.用于蛋白质组学和结构数据交互探索的计算工具。
Mol Cell Proteomics. 2010 Aug;9(8):1703-15. doi: 10.1074/mcp.R000007-MCP201. Epub 2010 Jun 4.
2
Structural genomics.结构基因组学
Methods Biochem Anal. 2003;44:591-612.
3
Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.Prequips——一个用于液相色谱-串联质谱蛋白质组学数据集成、可视化和分析的可扩展软件平台。
Bioinformatics. 2009 Mar 1;25(5):682-3. doi: 10.1093/bioinformatics/btp005. Epub 2009 Jan 6.
4
ProHits: integrated software for mass spectrometry-based interaction proteomics.ProHits：基于质谱的相互作用蛋白质组学的集成软件。
Nat Biotechnol. 2010 Oct;28(10):1015-7. doi: 10.1038/nbt1010-1015.
5
Trans-proteomic pipeline: a pipeline for proteomic analysis.跨蛋白质组学流程：一种用于蛋白质组学分析的流程。
Methods Mol Biol. 2010;604:213-38. doi: 10.1007/978-1-60761-444-9_15.
6
AVID: an integrative framework for discovering functional relationships among proteins.AVID：一个用于发现蛋白质间功能关系的综合框架。
BMC Bioinformatics. 2005 Jun 1;6:136. doi: 10.1186/1471-2105-6-136.
7
Recent developments in proteome informatics for mass spectrometry analysis.用于质谱分析的蛋白质组信息学的最新进展。
Comb Chem High Throughput Screen. 2009 Feb;12(2):194-202. doi: 10.2174/138620709787315508.
8
Proteomic Tools for the Analysis of Cytoskeleton Proteins.
Methods Mol Biol. 2016;1365:385-413. doi: 10.1007/978-1-4939-3124-8_23.
9
Pushing structural information into the yeast interactome by high-throughput protein docking experiments.通过高通量蛋白质对接实验将结构信息引入酵母相互作用组。
PLoS Comput Biol. 2009 Aug;5(8):e1000490. doi: 10.1371/journal.pcbi.1000490. Epub 2009 Aug 28.
10
Network Tools for the Analysis of Proteomic Data.用于蛋白质组学数据分析的网络工具
Methods Mol Biol. 2017;1549:177-197. doi: 10.1007/978-1-4939-6740-7_14.
引用本文的文献
1
Analysis Determining the Binding Interactions of NAD(P)H: Quinone Oxidoreductase 1 and Resveratrol via Docking and Molecular Dynamic Simulations.通过对接和分子动力学模拟确定NAD(P)H：醌氧化还原酶1与白藜芦醇结合相互作用的分析
Eur J Biol. 2023 Dec;82(2):280-288. doi: 10.26650/eurjbiol.2023.1352396. Epub 2023 Nov 23.
2
Ten simple rules to create biological network figures for communication.创作用于交流的生物网络图形的 10 个简单规则
PLoS Comput Biol. 2019 Sep 26;15(9):e1007244. doi: 10.1371/journal.pcbi.1007244. eCollection 2019 Sep.
3
Allosteric signalling in the outer membrane translocation domain of PapC usher.PapC 外膜转运结构域中的变构信号传导。
Elife. 2014 Oct 28;3:e03532. doi: 10.7554/eLife.03532.
4
Structural bioinformatics of the interactome.互作组学的结构生物信息学。
Annu Rev Biophys. 2014;43:193-210. doi: 10.1146/annurev-biophys-051013-022726.
5
Topological analysis and interactive visualization of biological networks and protein structures.生物网络和蛋白质结构的拓扑分析及交互式可视化。
Nat Protoc. 2012 Mar 15;7(4):670-85. doi: 10.1038/nprot.2012.004.
6
Interactive JIMD articles using the iSee concept: turning a new page on structural biology data.采用iSee概念的交互式《遗传性视网膜疾病杂志》文章：翻开结构生物学数据的新篇章。
J Inherit Metab Dis. 2011 Jun;34(3):565-7. doi: 10.1007/s10545-011-9334-4. Epub 2011 Apr 21.
本文引用的文献
1
Integrative structure modeling of macromolecular assemblies from proteomics data.从蛋白质组学数据中对大分子组装进行综合结构建模。
Mol Cell Proteomics. 2010 Aug;9(8):1689-702. doi: 10.1074/mcp.R110.000067. Epub 2010 May 27.
2
Toward an integrated structural model of the 26S proteasome.朝向 26S 蛋白酶体的整合结构模型。
Mol Cell Proteomics. 2010 Aug;9(8):1666-77. doi: 10.1074/mcp.R000002-MCP201. Epub 2010 May 13.
3
Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions.基于分水岭和尺度空间滤波的冷冻电镜密度图分割的定量分析，以及通过与区域配准来拟合结构。
J Struct Biol. 2010 Jun;170(3):427-38. doi: 10.1016/j.jsb.2010.03.007. Epub 2010 Mar 23.
4
Fibroblast growth factor signalling: from development to cancer.成纤维细胞生长因子信号通路：从发育到癌症。
Nat Rev Cancer. 2010 Feb;10(2):116-29. doi: 10.1038/nrc2780.
5
Proteome organization in a genome-reduced bacterium.基因组简化细菌中的蛋白质组组织
Science. 2009 Nov 27;326(5957):1235-40. doi: 10.1126/science.1176343.
6
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate.癌症相关的 IDH1 突变会产生 2-羟基戊二酸。
Nature. 2009 Dec 10;462(7274):739-44. doi: 10.1038/nature08617.
7
Predicting new molecular targets for known drugs.预测已知药物的新分子靶标。
Nature. 2009 Nov 12;462(7270):175-81. doi: 10.1038/nature08506. Epub 2009 Nov 1.
8
Survey of large protein complexes in D. vulgaris reveals great structural diversity.对寻常脱硫弧菌中大型蛋白质复合物的调查揭示了巨大的结构多样性。
Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16580-5. doi: 10.1073/pnas.0813068106. Epub 2009 Sep 11.
9
Three-dimensional structural view of the central metabolic network of Thermotoga maritima.嗜热栖热菌中心代谢网络的三维结构视图。
Science. 2009 Sep 18;325(5947):1544-9. doi: 10.1126/science.1174671.
10
Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology.人类蛋白质参考数据库和人类蛋白质百科全书作为系统生物学的发现工具。
Methods Mol Biol. 2009;577:67-79. doi: 10.1007/978-1-60761-232-2_6.
Zotero 插件