Input
10 credits
Output
Configure input settings on the left, then click "Submit job"
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Convert SDF ligand files, including multi-record batches, into SMILES strings.
Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Convert Protein Data Bank files to Structure Data Format
Convert Structure Data Format files to Protein Data Bank format
SMILES to InChI converts SMILES strings into InChI (International Chemical Identifier) strings using RDKit. InChI was developed by IUPAC and NIST as a canonical, non-proprietary chemical identifier. Unlike SMILES — which can represent the same molecule in multiple valid ways — InChI is fully canonical, meaning any two valid SMILES strings for the same molecule will always produce an identical InChI string. This makes InChI valuable for deduplication, database registration, and interoperability with systems that use InChI as a primary key, including ChEMBL and InChIKey-based lookup services.
InChIKey, a fixed-length 27-character hash derived from a full InChI string, is widely used for web searches and database lookups. This tool produces full InChI strings; InChIKey generation is a separate downstream step.
The tool accepts SMILES directly in the browser, supports file upload, and can also retrieve structures from PubChem by compound name or CID. Up to 10 entries are processed per job.
| Option | Details |
|---|---|
| SMILES strings | One SMILES per line, or name<TAB>SMILES pairs for named entries |
| File upload | .txt, .csv, .tsv, .smi, .smiles files |
| PubChem fetch | Compound names or CIDs for batch structure retrieval |
| File | Description |
|---|---|
| Per-entry InChI files | Individual InChI string for each input molecule |
batch.tsv | Combined tab-separated file with all input identifiers and their InChI strings |