Code for manuscript:

"Protein dynamics at different timescales unlock access to hidden post-translational modification sites"

Article preprint: https://www.biorxiv.org/content/10.1101/2025.06.25.661537v1

This project also uses code and SQL tables from AlphaSync (https://alphasync.stjude.org).

AlphaSync code: https://github.com/langbnj/alphasync.

AlphaSync preprint: https://www.biorxiv.org/content/10.1101/2025.03.12.642845v2.

analyses: R scripts used to perform statistical analyses and produce figures.

include: Utility functions.

mysql_tables: MySQL table structures (CREATE statements).

pipeline: Scripts used to extract and analyse data from data tables (SQL).

scripts: Additional utility scripts.

update: Scripts used to fill data tables (SQL).

For "pipeline" and "update", first run "download.py" (or "download.pl") to download datasets, followed by "run.py" (or "run.pl").

Create MySQL tables using "mysql_tables/create_statements.sql". Then, fill MySQL tables in this sequence:

• update/uniprot (UniProt version 2022_04)
• update/ensembl (Ensembl version 108)
• update/tax (NCBI taxonomy tables)
• update/compara (Ensembl Compara tables)
• update/comparanopara (Ensembl Compara tables, paralog-filtered)
• update/evolutionary_rate_rate4site (Rate4Site evolutionary rates)
• update/evolutionary_rate_lichtarge (real-valued Evolutionary Trace score, rvET)
• update/evolutionary_rate_capra (Capra et al. conservation scores, Jensen-Shannon Divergence)
• update/evolutionary_rate_sporadic_protein_removal (Remove a handful of proteins not fully covered by all conservation scoring methods)
• update/evolutionary_rate_normalize (Normalize conservation scores)

...followed by the other tables.

Please don't hesitate to contact me/us for questions and assistance with these scripts ([email protected]). They have grown historically as these analyses grew far more complex than originally envisioned, though we have done our best to comment them well enough to follow along and use them. Thank you!