What is SMILES to PDB?
SMILES to PDB converts SMILES strings into three-dimensional PDB format files using RDKit. While SMILES encodes molecular connectivity as a text string, PDB carries explicit 3D atomic coordinates, making it suitable for molecular visualization alongside protein structures in viewers such as PyMOL, VMD, and UCSF Chimera.
How to use SMILES to PDB online
ProteinIQ performs the conversion server-side, generating 3D coordinates and producing one PDB file per input compound without requiring RDKit or any local chemistry software.
Input
| Input type | Format details |
|---|
| SMILES strings | One SMILES per line, or name<TAB>SMILES pairs for named compounds |
| File upload | .txt, .csv, .tsv, .smi, .smiles files |
| PubChem fetch | Compound names or CIDs fetched in batch from PubChem |
| Batch limit | Up to 10 entries per job |
Settings
| Setting | Description |
|---|
Add hydrogens | Adds explicit hydrogens before 3D embedding (default: on). Recommended for accurate geometry. |
Optimize geometry | Runs a short UFF force field minimization after coordinate generation (default: on). Improves coordinate quality for strained or flexible structures. |
Output
Each input compound produces a separate PDB file containing 3D atomic coordinates, downloadable individually and ready to load into molecular visualization software alongside protein structures.
How it works
RDKit's AllChem.EmbedMolecule places atoms in 3D space using distance geometry. When Add hydrogens is enabled, Chem.AddHs is called first so hydrogen positions are included in the embedding. When Optimize geometry is enabled, a short Universal Force Field (UFF) minimization via AllChem.UFFOptimizeMolecule relaxes bond lengths, angles, and torsions. The resulting conformer is then written in PDB format.
Limitations
- A single conformer is generated per molecule — the global energy minimum is not guaranteed.
- PDB format does not store explicit bond orders or formal charges. For docking ligand preparation, SMILES to SDF or SMILES to MOL2 are the preferred formats because they retain this information.
- Tautomer and protonation state are taken as given from the input SMILES; no pH adjustment is applied.
- Very large or highly flexible macrocycles can fail distance geometry embedding.
