Clustering poses from ligand dockingΒΆ
This protocol uses ap_ligand_clustering program of the BioShell 3.0 1 package, which should be called as:
ap_ligand_clustering LIG list_of_files.txt min_cluster_size clustering_cutoff
e.g.
ap_ligand_clustering LIG list_of_files.txt 10 3.0
where LIG is the three-letter ligand PDB code and list_of_files.txt file contains names of output .pdb files, for example:
./out/protein_HEM_LIG.pdb_0.pdb
./out/protein_HEM_LIG.pdb_1.pdb
./out/protein_HEM_LIG.pdb_2.pdb
./out/protein_HEM_LIG.pdb_3.pdb
./out/protein_HEM_LIG.pdb_4.pdb
The two other parameters: min_cluster_size and clustering_cutoff control what clusters are created, i.e. their minimal size and distace cutoff, respectively. In the above example clusters of 10 or more structures will be written. Every cluster contains only these structures where their mutual distance is no longer than 3.0A.
For further information see also: https://bioshell.readthedocs.io/en/latest/examples/ap_ligand_clustering.html
References