Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins

David D. Holcomb; Katarzyna I. Jankowska; Nancy Hernandez; Kyle Laurie; Jacob Kames; Nobuko Hamasaki-Katagiri; Anton A A Komar; Michael DiCuccio; Chava Kimchi-Sarfaty

doi:10.1016/j.xpro.2022.101648

Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins

David D. Holcomb
, Katarzyna I. Jankowska
, Nancy Hernandez
, Kyle Laurie
, Jacob Kames
, Nobuko Hamasaki-Katagiri
, Anton A A Komar
, Michael DiCuccio
, Chava Kimchi-Sarfaty

Division of Plasma Protein Therapeutics Food and Drug Administration
National Institutes of Health

Research output: Contribution to journal › Article › peer-review

Abstract

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).

Original language	English
Article number	101648
Journal	STAR Protocols
Volume	3
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2022.101648
State	Published - Sep 16 2022

Keywords

Bioinformatics
Computer sciences
Genetics
Health sciences
Molecular biology

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10.1016/j.xpro.2022.101648

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Holcomb, D. D., Jankowska, K. I., Hernandez, N., Laurie, K., Kames, J., Hamasaki-Katagiri, N., Komar, A. A. A., DiCuccio, M., & Kimchi-Sarfaty, C. (2022). Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins. STAR Protocols, 3(3), Article 101648. https://doi.org/10.1016/j.xpro.2022.101648

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abstract = "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).",

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AU - Hernandez, Nancy

AU - Laurie, Kyle

AU - Kames, Jacob

AU - Hamasaki-Katagiri, Nobuko

AU - Komar, Anton A A

AU - DiCuccio, Michael

AU - Kimchi-Sarfaty, Chava

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Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins

Abstract

Keywords

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