Protein-Ligand Interaction Fingerprints¶

EasyDock can calculate protein-ligand interaction fingerprints (PLIFs) using ProLIF and compute similarity to reference interactions.

Calculate PLIFs¶

From Database¶

Calculate PLIFs for docked molecules:

easydock_plif -i output.db -p protein.pdb -c 4

Parameters:

• -i: Database with docked molecules
• -p: Protein PDB file with all hydrogens
• -c: Number of CPU cores

Output: PLIFs are stored in the database for later retrieval.

Specific Poses¶

By default, only top poses are processed. Specify other poses if needed and there were requested in docking setup:

easydock_plif -i output.db -p protein.pdb --poses 1 2 3 -c 4

From SDF Files¶

Calculate PLIFs directly from SDF (useful for reference ligands):

easydock_plif -i reference.sdf -p protein.pdb -o plif_output.txt -c 4

Retrieve PLIFs¶

Extract calculated PLIFs from database:

easydock_plif -i output.db -o plif_output.txt

Output format: Tab-separated file with 0 and 1.

Retrieve Specific Molecules¶

easydock_plif -i output.db -o plif_output.txt -d mol_1 mol_2 mol_3

PLIF Similarity¶

Compare PLIFs to reference interactions:

easydock_plif -i output.db -o similarity.txt \
    --ref_plif ala31.a.hydrophobic asp86.a.cationic

PLIF naming format: [residue_name][residue_number].[chain].[interaction_type]

Common interaction types:

• hydrophobic: Hydrophobic interaction
• hbdonor: Hydrogen bond donor
• hbacceptor: Hydrogen bond acceptor
• cationic: Cation-π interaction
• anionic: Anion-π interaction

Combined Operations¶

Calculate PLIFs and compare in one command:

easydock_plif -i output.db -p protein.pdb -o similarity.txt \
    --ref_plif ala31.a.hydrophobic asp86.a.cationic -c 4

Workflow Example¶

1. Get reference PLIF from known ligand:

   easydock_plif -i reference.sdf -p protein.pdb -o reference_plif.txt -c 4
   

2. Identify key interactions from output:

   # Example output:
   mol_ref: ala31.a.hydrophobic asp86.a.cationic
   

3. Calculate similarity for docked molecules:

   easydock_plif -i output.db -p protein.pdb -o similarity.txt \
       --ref_plif ala31.a.hydrophobic asp86.a.cationic -c 4
   

4. Extract top scoring by PLIF similarity:

   get_sdf_from_easydock -i output.db -o output.sdf \
       --fields plif_similarity \
       --add_sql 'plif_similarity > 0.8'
   

Important Notes¶