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G2S: a web-service for annotating genomic variants on 3D protein structures.G2S：一个用于在 3D 蛋白质结构上注释基因组变异的网络服务。
Bioinformatics. 2018 Jun 1;34(11):1949-1950. doi: 10.1093/bioinformatics/bty047.
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PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants.PhyreRisk：一个动态的 Web 应用程序，将基因组学、蛋白质组学和 3D 结构数据联系起来，指导人类遗传变异的解释。
J Mol Biol. 2019 Jun 14;431(13):2460-2466. doi: 10.1016/j.jmb.2019.04.043. Epub 2019 May 7.
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DBAli tools: mining the protein structure space.DBAli工具：挖掘蛋白质结构空间
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W393-7. doi: 10.1093/nar/gkm236. Epub 2007 May 3.
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Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.将基因组信息与RCSB蛋白质数据库中的蛋白质序列和三维原子水平结构相结合。
Bioinformatics. 2016 Dec 15;32(24):3833-3835. doi: 10.1093/bioinformatics/btw547. Epub 2016 Aug 22.
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VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.VarMap：一个将基因组坐标映射到蛋白质序列和结构并检索蛋白质结构注释的网络工具。
Bioinformatics. 2019 Nov 1;35(22):4854-4856. doi: 10.1093/bioinformatics/btz482.
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The new protein topology graph library web server.新型蛋白质拓扑结构图库网络服务器。
Bioinformatics. 2016 Feb 1;32(3):474-6. doi: 10.1093/bioinformatics/btv574. Epub 2015 Oct 6.
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G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures.G23D：用于在三维蛋白质结构上绘制和可视化基因组变异的在线工具。
BMC Genomics. 2016 Aug 26;17(1):681. doi: 10.1186/s12864-016-3028-0.
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The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.可视化CMAT：一个用于选择和解释蛋白质家族中相关突变/共同进化残基的网络服务器。
J Bioinform Comput Biol. 2018 Apr;16(2):1840005. doi: 10.1142/S021972001840005X. Epub 2017 Dec 28.
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I-PV: a CIRCOS module for interactive protein sequence visualization.I-PV：一个用于交互式蛋白质序列可视化的 CIRCOS 模块。
Bioinformatics. 2016 Feb 1;32(3):447-9. doi: 10.1093/bioinformatics/btv579. Epub 2015 Oct 10.
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FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.FuncPatch：一个用于快速贝叶斯推断蛋白质 3D 结构中保守功能斑块的网络服务器。
Bioinformatics. 2015 Feb 15;31(4):523-31. doi: 10.1093/bioinformatics/btu673. Epub 2014 Oct 15.
引用本文的文献
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Prediction of protein stability changes upon single-point variant using 3D structure profile.使用三维结构轮廓预测单点变体引起的蛋白质稳定性变化。
Comput Struct Biotechnol J. 2022 Dec 8;21:354-364. doi: 10.1016/j.csbj.2022.12.008. eCollection 2023.
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Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer.基因组 nexus：癌症基因组变异注释和解读的综合资源
JCO Clin Cancer Inform. 2022 Feb;6:e2100144. doi: 10.1200/CCI.21.00144.
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Conformational Changes of Glutamine 5'-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations.谷氨酰胺5'-磷酸核糖焦磷酸酰胺转移酶与两种底物类似物结合时的构象变化：来自传统分子动力学和加速分子动力学模拟的见解
Front Chem. 2021 Feb 26;9:640994. doi: 10.3389/fchem.2021.640994. eCollection 2021.
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MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization.MusiteDeep：一个基于深度学习的蛋白质翻译后修饰位点预测和可视化的网络服务器。
Nucleic Acids Res. 2020 Jul 2;48(W1):W140-W146. doi: 10.1093/nar/gkaa275.
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TGPred: a tumor gene prediction webserver for analyzing structural and functional impacts of variants.TGPred：一个用于分析变异体结构和功能影响的肿瘤基因预测网络服务器。
J Mol Cell Biol. 2020 Jul 1;12(7):556-558. doi: 10.1093/jmcb/mjaa007.
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PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants.PhyreRisk：一个动态的 Web 应用程序，将基因组学、蛋白质组学和 3D 结构数据联系起来，指导人类遗传变异的解释。
J Mol Biol. 2019 Jun 14;431(13):2460-2466. doi: 10.1016/j.jmb.2019.04.043. Epub 2019 May 7.
7
BioJava 5: A community driven open-source bioinformatics library.BioJava 5：一个社区驱动的开源生物信息学库。
PLoS Comput Biol. 2019 Feb 8;15(2):e1006791. doi: 10.1371/journal.pcbi.1006791. eCollection 2019 Feb.
本文引用的文献
1
3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets.癌症中体细胞突变的三维簇揭示了众多作为功能靶点的罕见突变。
Genome Med. 2017 Jan 23;9(1):4. doi: 10.1186/s13073-016-0393-x.
2
UniProt: the universal protein knowledgebase.通用蛋白质知识库：UniProt
Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169. doi: 10.1093/nar/gkw1099. Epub 2016 Nov 29.
3
G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures.G23D：用于在三维蛋白质结构上绘制和可视化基因组变异的在线工具。
BMC Genomics. 2016 Aug 26;17(1):681. doi: 10.1186/s12864-016-3028-0.
4
Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.将基因组信息与RCSB蛋白质数据库中的蛋白质序列和三维原子水平结构相结合。
Bioinformatics. 2016 Dec 15;32(24):3833-3835. doi: 10.1093/bioinformatics/btw547. Epub 2016 Aug 22.
5
A global reference for human genetic variation.人类遗传变异的全球参考。
Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393.
6
The Cancer Genome Atlas Pan-Cancer analysis project.癌症基因组图谱泛癌分析项目。
Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764.
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Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.利用 cBioPortal 进行复杂癌症基因组学和临床特征的综合分析
Sci Signal. 2013 Apr 2;6(269):pl1. doi: 10.1126/scisignal.2004088.
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SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.SIFTS：结构整合与功能、分类学和序列资源。
Nucleic Acids Res. 2013 Jan;41(Database issue):D483-9. doi: 10.1093/nar/gks1258. Epub 2012 Nov 29.
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The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.cBio 癌症基因组学门户：一个用于探索多维癌症基因组学数据的开放平台。
Cancer Discov. 2012 May;2(5):401-4. doi: 10.1158/2159-8290.CD-12-0095.
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BioJava: an open-source framework for bioinformatics.BioJava：一个用于生物信息学的开源框架。
Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8.
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