How to Prepare Ligand Library

Preparing Your Downloaded Ligand Library

The downloaded file may need further processing depending on the requirements of your molecular modeling software. This might involve:

• Format Conversion: Using tools like Open Babel to convert between different file formats.

• Protonation and Tautomer Generation: Ensuring the molecules are in the correct protonation state and considering relevant tautomeric forms at a physiological pH. Software like Open Babel or specialized molecular modeling packages can perform these tasks.

• 3D Coordinate Generation: If you downloaded SMILES strings, you will need to generate 3D coordinates for the molecules using software like Open Babel or CORINA.

Cleaning and Converting Ligands

Before docking or QSAR analysis, ligands may require:

• Energy minimization

• Format conversion

• Protonation state adjustment (pH 7.4)

• Tautomer cleanup

🔧 You can use tools like:

• Open Babel (command-line or GUI)

• RDKit (for Python workflows)

• PyRx or AutoDockTools for docking prep

NOTE

Another Tutorial will be provided on how to use the Open babel for Cleaning and Converting Ligands, for molecular docking using the PyRx software, we don't need to use the open babel for the ligand cleaning and converting.

Visualizing Ligands (Optional but Helpful) 

Use PyMOL, Chimera, or Discovery Studio to visualize 3D structures.

Check for steric clashes, tautomers, or missing hydrogens before docking.

The PubChem database offers a vast amount of information and is widely used. The tutorials above provide just a few examples of the PubChem database's usage. Subsequent tutorials will cover additional database usage.

REFERENCES

1. PubChem: National Center for Biotechnology Information (NCBI). Retrieved from PubChem 

2. Kim S. et al. (2021). PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Research, 49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971