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Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins.
Holcomb, David D; Jankowska, Katarzyna I; Hernandez, Nancy; Laurie, Kyle; Kames, Jacob; Hamasaki-Katagiri, Nobuko; Komar, Anton A; DiCuccio, Michael; Kimchi-Sarfaty, Chava.
  • Holcomb DD; Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA. Electronic address: holcombddf@gmail.com.
  • Jankowska KI; Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA.
  • Hernandez N; Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA.
  • Laurie K; Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA.
  • Kames J; Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA.
  • Hamasaki-Katagiri N; Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA.
  • Komar AA; Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA.
  • DiCuccio M; National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
  • Kimchi-Sarfaty C; Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA. Electronic address: chava.kimchi-sarfaty@fda.hhs.gov.
STAR Protoc ; 3(3): 101648, 2022 09 16.
Article in English | MEDLINE | ID: covidwho-1967230
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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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Prognostic study Topics: Variants Limits: Humans Language: English Journal: STAR Protoc Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Prognostic study Topics: Variants Limits: Humans Language: English Journal: STAR Protoc Year: 2022 Document Type: Article