Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins
Summary: 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 p...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722005287 |
| _version_ | 1828743248899735552 |
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| author | David D. Holcomb Katarzyna I. Jankowska Nancy Hernandez Kyle Laurie Jacob Kames Nobuko Hamasaki-Katagiri Anton A. Komar Michael DiCuccio Chava Kimchi-Sarfaty |
| author_facet | David D. Holcomb Katarzyna I. Jankowska Nancy Hernandez Kyle Laurie Jacob Kames Nobuko Hamasaki-Katagiri Anton A. Komar Michael DiCuccio Chava Kimchi-Sarfaty |
| author_sort | David D. Holcomb |
| collection | DOAJ |
| description | Summary: 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 Holcomb et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-13T01:33:28Z |
| format | Article |
| id | doaj.art-a7839a0221ce406ea1d8b57270cee8d1 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-13T01:33:28Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-a7839a0221ce406ea1d8b57270cee8d12022-12-22T03:08:27ZengElsevierSTAR Protocols2666-16672022-09-0133101648Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteinsDavid D. Holcomb0Katarzyna I. Jankowska1Nancy Hernandez2Kyle Laurie3Jacob Kames4Nobuko Hamasaki-Katagiri5Anton A. Komar6Michael DiCuccio7Chava Kimchi-Sarfaty8Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA; Corresponding authorCenter for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USACenter for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USACenter for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USACenter for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USACenter for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USACenter for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USANational Center of Biotechnology Information, National Institutes of Health, Bethesda, MD, USACenter for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA; Corresponding authorSummary: 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 Holcomb et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722005287BioinformaticsHealth sciencesGeneticsMolecular biologyComputer sciences |
| spellingShingle | David D. Holcomb Katarzyna I. Jankowska Nancy Hernandez Kyle Laurie Jacob Kames Nobuko Hamasaki-Katagiri Anton A. Komar Michael DiCuccio Chava Kimchi-Sarfaty Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins STAR Protocols Bioinformatics Health sciences Genetics Molecular biology Computer sciences |
| title | Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins |
| title_full | Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins |
| title_fullStr | Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins |
| title_full_unstemmed | Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins |
| title_short | Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins |
| title_sort | protocol to identify host viral protein interactions between coagulation related proteins and their genetic variants with sars cov 2 proteins |
| topic | Bioinformatics Health sciences Genetics Molecular biology Computer sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722005287 |
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