Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles

The dataset contains the data used in the paper "Improved structural modelling of antibodies and their complexes with clustered diffusion ensembles". More specifically, the following files are available:

• colabfold.zip : list of colabfold_batch results for the 54 antibodies discussed in the manuscript
• alphaflow.zip : directory containing AlphaFlow ensembles for the 54 antibodies discussed in the manuscript (1000 models per PDB)
• colabfold_antigen.zip : directory containing the colabfold_batch results for the 17 PDBs with low H3 loop PLDDT (low-80 dataset, see manuscript). Here the sequence of the antigen is also provided.
• clustered_alphaflow_ensembles.zip : directory containing all the used clustered AlphaFlow ensembles for the 17 PDBs part of the LOW-80 dataset.
• 7*.tgz : files with all the docking runs described in the manuscript

several bash script are also available. They allow one to reproduce the results obtained in the paper.

In order to use them:

1. clone the repository https://github.com/haddocking/alphaflow-antibodies/ and follow the installation instructions
2. download all the zip and script files in the data directory of the downloaded repository (https://github.com/haddocking/alphaflow-antibodies/tree/main/data)
3. unzip the compressed zip files
4. execute the scripts in this order:
   • colabfold_analysis_cmds.sh / colabfold_heavy_analysis_cmds
   • colabfold_antigen_analysis_cmds / colabfold_antigen_heavy_analysis_cmds
   • alphaflow_analysis_cmds
   • alphaflow_clustered_ensemble_lines