Genotype-by-Inhibitor Interactions to Dissect Enterovirus Replication - Bakhache, Orr, and Dolan. (2025)

Repository Contents

This repository contains all files, scripts, and structural predictions used in the paper.

.
├── 1.Figures
│   ├── Figure_1.ai
│   ├── Figure_2.ai
│   ├── Figure_3.ai
│   ├── Figure_4.ai
│   ├── Figure_5.ai
│   ├── Supplementary Figure_1.ai
│   ├── Supplementary Figure_2.ai
│   ├── Supplementary Figure_3.ai
│   ├── Supplementary Figure_4.ai
│   ├── Supplementary Figure_5.ai
│   ├── Supplementary Figure_6.ai
│   ├── Supplementary Figure_7.ai
│   └── Supplementary Figure_8.ai
├── 2.R_Scripts
│   ├── R_Script_Inhibitory_concentration_Analysis
│   ├── R_Script_Main_Figures_Analysis
│   └── R_Script_Replicon_Enriched_Variants
├── 3.Structures
│   ├── 1.2A_3C_Enrichment_Mapping_Rupi
│   ├── 2.2C_Enrichment_Mapping_BrefA_Guan
│   ├── 3.3A_Enrichment_Mapping_BrefA_Envi
│   └── README.md
└── README.md

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1. Figures

• .ai and .png files used in the manuscript.

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2. R Scripts

• "R_Script_Inhibitory_concentration_Analysis": Calculates different inhibitory concentrations (ICs) of inhibitors
• "R_Script_Main_Figures_Analysis": Performs analysis and generates the main figures for the manuscript
• "R_Script_Replicon_Enriched_Variants": Performs analysis and generates the figures for the replicon assays

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3. Structural Predictions

• "2A_3C_Enrichment_Mapping_Rupi": Mapping of enriched variants on 2A and 3C structure predictions in Rupintrivir conditions
• "3A_Enrichment_Mapping_BrefA_Envi": Mapping of enriched variants on 3A–host predictions in Brefeldin A and Enviroxime conditions
• "2C_Enrichment_Mapping_BrefA_Guan": Mapping of Guanidine hydrochloride and Brefeldin A enrichment on 2C predicted structure and host factor interaction