Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins.
Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins.
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DOI：
10.1016/j.xpro.2022.101648
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发表时间：
2022-09-16
期刊：
影响因子：
--
通讯作者：
Kimchi-Sarfaty, Chava
中科院分区：
文献类型：
--
作者：
Holcomb, David D.;Jankowska, Katarzyna I.;Hernandez, Nancy;Laurie, Kyle;Kames, Jacob;Hamasaki-Katagiri, Nobuko;Komar, Anton A.;Dicuccio, Michael;Kimchi-Sarfaty, Chava
在这里，我们描述了一个生物信息学管道，评估凝血相关蛋白和遗传变异与SARS-CoV-2蛋白之间的相互作用。该管道搜索可能与病毒蛋白结合的宿主蛋白，并识别和评分蛋白质遗传变异，以预测特定亚群中的疾病发病机制。此外，它能够找到结构相似的基序，并确定宿主-病毒蛋白复合物内的潜在结合位点，以揭示病毒对受调控的生物过程的影响和/或宿主-蛋白对病毒入侵或繁殖的影响。有关本方案使用和执行的完整详细信息，请参阅。Pipeline识别与SARS-CoV-2蛋白相互作用的凝血相关蛋白Pipeline在COVID-19 HGI等数据库中搜索宿主蛋白遗传变异体基于大量计算机工具对选定的宿主蛋白遗传变异体进行评分在病毒-宿主系统中发现蛋白相互作用的相似基序和区域进行任何实验方案都需要遵守当地实验室安全和伦理的机构指南。在这里，我们描述了一个生物信息学管道，评估凝血相关蛋白和遗传变异与SARS-CoV-2蛋白之间的相互作用。该管道搜索可能与病毒蛋白结合的宿主蛋白，并识别和评分蛋白质遗传变异，以预测特定亚群中的疾病发病机制。此外，它能够找到结构相似的基序，并确定宿主-病毒蛋白复合物内的潜在结合位点，以揭示病毒对受调控的生物过程的影响和/或宿主-蛋白对病毒入侵或繁殖的影响。
Here, we describe a bioinformatics pipeline that evaluates the interactions between coagulation-related proteins and genetic variants with SARS-CoV-2 proteins. This pipeline searches for host proteins that may bind to viral protein and identifies and scores the protein genetic variants to predict the disease pathogenesis in specific subpopulations. Additionally, it is able to find structurally similar motifs and identify potential binding sites within the host-viral protein complexes to unveil viral impact on regulated biological processes and/or host-protein impact on viral invasion or reproduction. For complete details on the use and execution of this protocol, please refer to. Pipeline identifies coagulation-related proteins that interact with SARS-CoV-2 proteins The pipeline searches databases such as COVID-19 HGI for host protein genetic variants Score selected host-protein genetic variants based on numerous in silico tools Finds similar motifs and regions of protein-protein interaction in viral-host system Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Here, we describe a bioinformatics pipeline that evaluates the interactions between coagulation-related proteins and genetic variants with SARS-CoV-2 proteins. This pipeline searches for host proteins that may bind to viral protein and identifies and scores the protein genetic variants to predict the disease pathogenesis in specific subpopulations. Additionally, it is able to find structurally similar motifs and identify potential binding sites within the host-viral protein complexes to unveil viral impact on regulated biological processes and/or host-protein impact on viral invasion or reproduction.
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影响因子：
14.9
作者：
Cartegni, L;Wang, JH;Krainer, AR
通讯作者：
Krainer, AR
影响因子：
4.3
作者：
Holcomb D;Alexaki A;Hernandez N;Hunt R;Laurie K;Kames J;Hamasaki-Katagiri N;Komar AA;DiCuccio M;Kimchi-Sarfaty C
通讯作者：
Kimchi-Sarfaty C
影响因子：
64.8
作者：
COVID-19 Host Genetics Initiative
通讯作者：
COVID-19 Host Genetics Initiative
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
7
作者：
Ke, Shengdong;Shang, Shulian;Chasin, Lawrence A.
通讯作者：
Chasin, Lawrence A.