Scripts and data for Cisneros et al., (2024). Mutational biases promote neutral increases in the complexity of protein interaction networks following gene duplication.

Folders contain the following:

• Data: It contains folders to store the raw PDB files and intermediate files created by the data preparation steps, such as the CD-Hit sequence clustering, the DSSP secondary structure analysis, and the matrices with the distributions of mutational effects. The following data should be downloaded from their respective databases:

  . ECOD data: Should be stored in the Data/Structures folder. The ecod_latest.domains file should be downloaded from: http://prodata.swmed.edu/ecod/

  . PDB data: All the structure files should be stored in the Data/PDB/All_structures folder. Structures and the pdb_seqres.txt file should be downloaded from: https://www.rcsb.org/docs/programmatic-access/file-download-services#pdb-entry-files

• Figures: pdf versions of the main and supplementary figures

• Scripts: Contains scripts for data preparation, analysis, and figure generation. Folders and scripts are numbered according to the order in which they were used in the analysis.

• Results_simulations: Use this folder to store the results of the simulations. This folder will contain the Results_pdup1 from Zenodo once it is decompressed. The two subfolders inside contain the results of the different simulations for both the parametric and single structure regimes.

• Results_solution_space: Use this folder to store the results of our exploration of the solution space of the system of equations. These can be downloaded from Zenodo and decompressed.

A helper repository with large files should be downloaded from Zenodo (https://zenodo.org/records/10048861). The data from this repository should be uncompressed and organized as follows:

• all_mut_matrices.tsv: Should be uncompressed and moved to Homomer_duplication_2024/Data
• Results_pdup1: Should be uncompressed and moved to Homomer_duplication_2024/Results_simulations
• Results_solution_space: Should be uncompressed and moved to Homomer_duplication_2024
• Structures: Should be uncompressed and moved to Homomer_duplication_2024/Data