examples/README.md

Example Files for Docking@HOME

This directory contains example ligand and receptor files in PDBQT format for testing the Docking@HOME platform.

Files

example_ligand.pdbqt

• Type: Small molecule ligand
• Format: PDBQT (AutoDock format with partial charges and atom types)
• Rotatable Bonds: 2
• Atoms: 5
• Purpose: Simple test ligand for quick docking runs

example_receptor.pdbqt

• Type: Protein receptor
• Format: PDBQT
• Residues: 4 (ALA, GLY, VAL, LEU)
• Atoms: 24
• Purpose: Simple test receptor for demonstration

How to Use

Web GUI

1. Start the server:

   python start.py
   

2. Open browser to http://localhost:8080

3. Upload files:

   • Click "Choose File" for Ligand → Select example_ligand.pdbqt
   • Click "Choose File" for Receptor → Select example_receptor.pdbqt

4. Configure parameters:

   • Runs: 100 (or your choice)
   • GPU: Enable if available

5. Click "🚀 Start Docking"

Command Line

docking-at-home dock \
  -l examples/example_ligand.pdbqt \
  -r examples/example_receptor.pdbqt \
  -n 100 \
  --gpu

Python API

from docking_at_home.server import job_manager, initialize_server
import asyncio

async def main():
    await initialize_server()
    
    job_id = await job_manager.submit_job(
        ligand_file="examples/example_ligand.pdbqt",
        receptor_file="examples/example_receptor.pdbqt",
        num_runs=100,
        use_gpu=True
    )
    
    print(f"Job submitted: {job_id}")

asyncio.run(main())

Expected Results

When running docking with these example files, you should expect:

• Binding Energies: -12 to -6 kcal/mol (simulation mode)
• Poses: As many as requested runs
• Execution Time:
  • Simulation mode: ~1-2 seconds for 100 runs
  • Real AutoDock (CPU): ~30-60 minutes for 100 runs
  • Real AutoDock (GPU): ~2-5 minutes for 100 runs

Converting Your Own Files

These example files are in PDBQT format. To convert your own PDB files:

Using AutoDockTools (Python 2.7)

# Install AutoDockTools
pip install numpy
# Download from: http://autodock.scripps.edu/downloads

# Prepare ligand
pythonsh prepare_ligand4.py -l molecule.pdb -o molecule.pdbqt

# Prepare receptor
pythonsh prepare_receptor4.py -r protein.pdb -o protein.pdbqt

Using Open Babel

# Install Open Babel
# Ubuntu/Debian: sudo apt-get install openbabel
# Mac: brew install open-babel
# Windows: Download from http://openbabel.org/

# Convert ligand (add hydrogens and charges)
obabel molecule.pdb -O molecule.pdbqt -h --partialcharge gasteiger

# Convert receptor
obabel protein.pdb -O protein.pdbqt -h

Using PyMOL

# In PyMOL
load molecule.pdb
h_add
save molecule.pdbqt

File Format Details

PDBQT Format

PDBQT is an extension of PDB format that includes:

• Atom types (C.3, N.pl3, O.2, etc.)
• Partial charges (Gasteiger or other methods)
• Rotatable bonds (TORSDOF)
• Flexible residues (for receptor flexibility)

Example PDBQT Structure:

REMARK  Name = Example Ligand
REMARK  2 active torsions
ROOT
ATOM      1  C   UNL     1       0.000   0.000   0.000  0.00  0.00    +0.000 C 
ATOM      2  C   UNL     1       1.540   0.000   0.000  0.00  0.00    +0.000 C 
ENDROOT
BRANCH   2   3
ATOM      3  C   UNL     1       2.078   1.421   0.000  0.00  0.00    +0.000 C 
ENDBRANCH   2   3
TORSDOF 2

Key elements:

• REMARK: Comments and metadata
• ROOT/ENDROOT: Non-rotatable core structure
• BRANCH/ENDBRANCH: Rotatable bonds
• TORSDOF: Number of rotatable bonds (degrees of freedom)
• Coordinates: X, Y, Z in Ångströms
• Charges: Partial atomic charges

More Examples

For more example structures:

1. PDB Database: https://www.rcsb.org/

   • Download crystal structures
   • Convert to PDBQT

2. PubChem: https://pubchem.ncbi.nlm.nih.gov/

   • Download small molecules
   • Convert to PDBQT

3. AutoDock Website: https://autodock.scripps.edu/

   • Example files
   • Tutorials
   • Documentation

Troubleshooting

File Not Recognized?

Make sure your PDBQT file has:

• .pdbqt extension
• Proper ATOM/HETATM records
• Gasteiger charges
• Correct atom types

Invalid Coordinates?

Check that:

• Coordinates are in Ångströms
• Values are reasonable (not NaN or infinity)
• Structure is 3D (not 2D)

Missing Charges?

Add charges using:

obabel input.pdb -O output.pdbqt --partialcharge gasteiger

Support

• 📧 Email: [email protected]
• 🤗 Issues: https://huggingface.co/OpenPeerAI/DockingAtHOME/discussions
• 📚 AutoDock Docs: https://autodock.scripps.edu/

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Authors: OpenPeer AI, Riemann Computing Inc., Bleunomics, Andrew Magdy Kamal