This is a repository of protein-ligand complexes prepared for docking in PDB nad PDBQT formats.
The detailed pipeline is described in the document Target-prepare_desgn.docx. Please follow it if you contribute a new structure.
The major feature is that all structures of an individual protein are aligned and a single grid box is used for all of them.
The repository is composed of directories for individual proteins, where every directory has the following structure:
UNIPROT_ID (protein)
|-PDB_ID_1 (particular complex)
| |-CHAIN_ID (particular chain)
| |-.._protein.pdb (prepared protein)
| |-.._protein.pdbqt (prepared protein)
| |-.._ligand.pdb (prepared ligand)
| |-.._liagnd.mol(sdf) (prepared ligand)
| |-.. (other files can be presented)
|-PDB_ID_2
| |-CHAIN_ID
| |-.._protein.pdb
| |-.._protein.pdbqt
| |-.._ligand.pdb
| |-.._liagnd.mol(sdf)
|-box.txt (grid box, may have different names)
|-info.txt (auxillary information)
The directory scripts contains some useful scripts for protein preparation.