Computational protocol: A computationally driven analysis of the polyphenol-protein interactome

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Protocol publication

[…] To query small molecule-protein interaction databases, the polyphenol list was searched in CHEBI database, containing ~100,000 entries, for corresponding CHEBI ID’s based on standardised SMILES. Polyphenol-protein interactions were mined from the STITCH, Pathway Commons and BindingDB databases, which collect information from multiple and often redundant databases, using name and CHEBI ID. Depending on the database, the term ‘interaction’ can either refer to direct binding (most interactions in STITCH and Pathway Commons and all interactions in BindingDB) or indirect interactions. STITCH also details the type of evidence (i.e. experimental, database, prediction, text mining) and the confidence score associated to each interaction listed. The confidence score ranged from 0.15 (low evidence) to 0.9 (highest evidence). Interactions based solely on text mining evidence or with confidence score <0.9 were excluded.The proteins obtained from these searches were analysed with DAVID tools for Functional Annotation Clustering using InterPro (Protein sequence analysis & classification) for protein clustering and classification. Enrichment scores >3 were considered.The quercetin and metabolites – protein interactomes were constructed as a network using Cytoscape v.4.3.0. The organic micronutrient-protein interactome was mined from STITCH, excluding interactions based solely on text mining and those with evidence scores <0.7. The metformin-protein interactome was obtained using the same methodology but excluding interactions with evidence score <0.9. […]

Pipeline specifications

Software tools DAVID, InterPro
Databases ChEBI Pathway Commons BindingDB
Application Protein sequence analysis
Chemicals Phenol, Polyphenols