Welcome to the GitHub repository for the following publication: [Allosteric and Energetic Remodeling of a PDZ domain by Protein Domain Extensions (Cristina Hidalgo-Carcedo, Andre J. Faure, Aina Martí-Aranda, Taraneh Zarin and Ben Lehner 2026). Here you'll find source code for computational analyses and to reproduce the figures in the paper.
Please download and untar/unzip the required data from https://doi.org/10.5281/zenodo.16411462 to your "base_dir" folder for running the analysis
The code is ran on RMarkdown This code was last run and tested with Mac OSX and with R version 4.5.0 (2025-04-11)
The following packages are required (package_version):
- data.table_1.17.2
- ggplot2_3.5.2
- ggpubr_0.6.0
- readxl_1.4.5
- dplyr_1.1.4
- ggtext_0.1.2
- scales_1.4.0
- GGally_2.2.1
- Cairo_1.6-2
- ggrastr_1.0.2
- ggrepel_0.9.6
- tidyr_1.3.1