Root Directory:
    a2a_l.sdf: Reference (co-crystalised) ligand used to define binding pocket (from DEKOIS, DUD-E or lit-pcba databases).
    a2a_p.pdb: The input protein structure file in PDB format (from DEKOIS, DUD-E or lit-pcba databases).
    docking_library.sdf: The library of compounds to be docked (from DEKOIS, DUD-E or lit-pcba databases).

a2a_p_protoss Directory:
    Files:
        allposes.sdf: Contains all poses generated during docking.
        final_library.sdf: The final set of protonated and minimised compounds before docking.
        
    Subdirectories:
        clustering: Contains clustered docking poses using various methods present in DockM8.
            3DScore_clustered.sdf
            ConvexPLR_clustered.sdf
            KORP-PL_clustered.sdf
            RMSD_clustered.sdf
            RTMScore_clustered.sdf
            bestpose_GNINA_clustered.sdf
            bestpose_PLANTS_clustered.sdf
            bestpose_QVINA2_clustered.sdf
            bestpose_QVINAW_clustered.sdf
            bestpose_SMINA_clustered.sdf
            bestpose_clustered.sdf
            espsim_clustered.sdf
            spyRMSD_clustered.sdf
            
        gnina: Contains GNINA docking results.
            gnina_poses.sdf
            
        plants: Contains PLANTS docking results.
            plants_poses.sdf
            
        qvina2: Contains QVina2 docking results.
            qvina2_poses.sdf
            
        qvinaw: Contains QVina-W docking results.
            qvinaw_poses.sdf
            
        smina: Contains SMINA docking results.
            smina_poses.sdf
            
        performance: Performance metrics.
            performance.csv
            
        rescoring_X_clustered: Contains rescoring results for different clustered methods.
            Each subdirectory (rescoring_3DScore_clustered, rescoring_ConvexPLR_clustered, etc.) contains:
                Rescoring results from various scoring functions (e.g., AD4_scores.csv, CHEMPLP_scores.csv, etc.).
                allposes_rescored.csv: Combined rescoring results for all poses.
                
Additional Protein Files:
    a2a_p_protoss.pdb: Protonated protein structure (using Protoss server).
    a2a_p_protoss_pocket.pdb: Trimmed protein (only binding site).
    a2a_p_protoss_pocket.pdbqt: Pocket structure in PDBQT format.