af_cubic_docking

This repository contains data available and explanations of them for the article:

Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking, Mads Jeppesen and Ingemar André

Larger files are deposited on Zenodo and referenced correspondingly here.

The repository for EvoDOCK (The software used to run all the simulations) are found on: https://github.com/Andre-lab/evodock.

The repository also explains how to set up all the necessary input files as well as how to run the simulations as done in the article.

Analysis of 111 cubic sequences by AF/AFM

The file 111_cubic_sequence_analysis.csv contains the results of the AF/AFM analysis. It contains the following entries:

• pdbid: The PDB id.
• symmetry: The symmetry of the PDB.
• fold: The fold type that was analysed and run with AF/AFM. "hf" stands for the higheset fold. That is the symmetric fold with the highest number. Two 2-folds were analyzed and are called 2_1 and 2_2 respectively.
• multimer: If the row values come from an AFM run.
• best RMSD: The best RMSD found among all the AF/AFM predictions compared to all native folds.
• best avg plddt: best average plddt found from all AF/AFM predictions.
• best iptm+ptm: best ipTM+pTM found from all AFM predictions.
• best ptm: best pTM found from all AFM predictions.
• best iptm: best ipTM found from all AFM predictions.
• best RMSD comes from mer: Which native fold the matches the prediction the best and gives rise to the value in best RMSD.
• symmetrizable: If the prediction is symmetrizable with Rosetta
• sym best total rmsd: The RMSD of the Rosetta symmetrized structure compared to the prediction.

All metric values for Reassembly docking and Complete assembly docking using an EvoDOCK ensemble

The file complete_assembly_and_reassembly_metric_data.csv contains all metric values from the Reassembly and Complete assembly docking simulations.

It contains the following entries:

• Symmetry: The symmetry of the structure
• pdbid: The PDB id of the structrure.
• docking type: If the simulation was Reassembly or Complete assembly docking.
• TMscore: The TM-score of the structure
• DockQ: The DockQ score of the structure
• RMSD: The RMSD of the structure
• type: if the values come from the Best Ranked or the Best Cluster

Initial structure lists from the RCSB

The initial list of homomeric I/O/T PDB files downloaded from RCSB is deposited here and is called initial_rcsb_list.tar.gz

Predicted structures from the method

The PDB files of the predicted structures for the Reassembly docking is deposited here and is called reassembly.tar.gz

The PDB files of the predicted structures for the Complete assembly docking is deposited here and is called complete_assembly.tar.gz