Download structures from the following data banks:

• AlphaFold Protein Structure Database by Google DeepMind and EMBL-EBI: fetch protein structures predicted by AlphaFold in PDBx/mmCIF format.
• Crystallography Open Database: fetch crystal structures in CIF format. The Crystal Creator extension is required to use this option.
• ESM Metagenomic Atlas by Meta AI: fetch protein structures predicted by ESMFold in PDB format.
• RCSB Protein Data Bank: fetch protein and ligand structures in PDB and/or PDBx/mmCIF formats.
• PubChem database at the National Institutes of Health (NIH): fetch small molecule structures based on PubChem CID identifiers.

Convert structures:

• Convert IUPAC names to SMILES using OPSIN at the Centre for Molecular Informatics at the University of Cambridge and EMBL-EBI.
• Convert SMILES codes to atomic structures using the RDKit library and then minimize them in SAMSON using the integrated minimizer with the Universal Force Field (UFF).