Residues Neighboring an SH3-Binding Motif Participate in Determining Affinity and Specificity In Vivo
All scripts and code for figures for Jordan et al 2024 https://doi.org/10.1101/2024.05.13.593936
This repo is designed to be used with the data contained in the folowing Dryad repository: https://doi.org/10.5061/dryad.79cnp5j3z. Both folders from Github and the Data folder from Dryad should be placed in the same folder, the paths in the scripts should work.
The figures folder contains R Markdown documents, that were used to generate all main and supplementary figures.
The scripts folder contains all scripts used in the analysis of the data collected in the manuscript. It is seperated into 3 sections :
- sequencing_analysis contains the scripts involved in processing the sequencing data, and obtaining read counts for every mutant in every sequencing library
- DHFR_PCA_analysis contains scripts that process the data from the DHFR-PCA experiments, including the sequencing data. It also has a script for the DHFR-PCA on solid media and the DHFR-PCA growth curves
- AlphaFold contains the script used to predict structures using AlphaFold-Multimer and the package requirements folder used