Hello! I am trying to construct a new data set of protein-ligand complexes labeled with affinity data. The plan is to extract features from the protein-ligand complex. But to do that I need to clean the complex structure.

I wonder what are the community favorite pipelines and open source programs to prepare/clean pdb files?

Cleaning / preparing the pdb file can mean that I need to do the following: Add missing heavy atoms / hydrogen atoms. Build missing loops. Convert non-standard residues to their standard equivalents. Select a single position for atoms with multiple alternate positions listed. Delete unwanted chains from the model. Delete unwanted heterogens.

Looking forward to read about your approaches!