README

Python script samples:

class_AF_output_processing.py - A script for processing AlphaFold-Multimer outputs. Along with regular pLDDT and PAE parsing, it includes custom analysis for sub-domains using pLDDT. It then parses residues within sub-domains for low PAE score regions. Any residues not meeting the confidence threshold are trimmed in the final structure, which are processed with the postprocess_pdbs.py script.

metrics_analysis.py - Parses AlphaFold outputs from the above script to generate a pairwise relationship plot for all metrics considered (PAE, pLDDT, average PAE, inter- and intra-chain PAE averages, among others).

Bash scripts Samples:

AFruns_process_automated.sh and run_AFruns_process_automated.sh automate handling post AlphaFold-Multimer run files. This includes automated trimming of output files to retain only necessary metrics and transferring files to permanent directories.

Others: rcsb_api_search.py - This script uses the RCSB API to query and process various ligands and proteins from the database directly.