Free online chemistry and sequence tools
Convert chemical file formats, calculate molecular properties, draw 2D structures, generate 3D conformers, search substructures with SMARTS and compute similarity — plus FASTA/FASTQ utilities and IUPAC name resolution. No registration, no install, no limits.
Format Converter
Convert between SMILES, InChI, MOL, SDF, PDB, XYZ, CML, MOL2 and 190+ more chemical file formats.
Molecular Properties
Molecular weight, formula, logP, TPSA, hydrogen bond donors/acceptors, rotatable bonds, InChIKey.
2D Structure Depiction
Turn a SMILES or InChI into a clean 2D skeletal structure image (SVG) you can download.
3D Structure Generator
Generate and rotate an interactive 3D conformer from any SMILES, and export it as SDF.
Substructure Search
Find molecules containing a SMARTS pattern. Paste a list and get every match instantly.
Molecular Similarity
Compare two molecules with Tanimoto similarity using FP2, FP3, FP4 or MACCS fingerprints.
Name to Structure
Turn an IUPAC name into a structure — SMILES, InChI, InChIKey and a drawn image.
Drug-likeness Checker
Evaluate Lipinski's rule of five and Veber rules: MW, logP, HBD, HBA, TPSA, rotatable bonds.
Batch Converter
Convert a whole compound library at once — upload an SDF or paste a SMILES list.
Formula & Weight
Molecular weight and elemental composition from a formula, or formula from a structure.
FASTA / FASTQ Tools
Sequence format conversion, GC content, reverse complement and DNA to protein translation.
Popular conversions
- SMILES to InChI converter — canonical IUPAC identifier
- InChI to SMILES converter — recover an editable SMILES
- SDF to SMILES converter — flatten a compound library
- MOL to SMILES converter — single-molecule MOL files
- SMILES to SDF converter — with 3D coordinates
- SMILES to PNG — structure images
- Lipinski rule of five calculator — drug-likeness check
What is SeqChem?
SeqChem wraps several open-source tools behind a simple web interface. OpenBabel — the chemistry toolbox used by researchers worldwide — handles every conversion, descriptor calculation and structure generation, so you get the same results as the command line without installing anything. OPSIN parses IUPAC names, with PubChem as a fallback for trivial names, and the sequence tools are implemented natively in Python.
Common workflows
- SMILES → InChI / InChIKey — standardise structures for databases and patents.
- SMILES → 3D SDF — generate a conformer for docking or visualisation.
- SDF → SMILES — flatten a structure file into a one-line representation.
- SMARTS substructure search — filter a compound list by functional group.
- Tanimoto similarity — cluster or deduplicate a screening library.
Why use it?
- No account, no paywall, no usage limit
- 190+ molecule formats supported by OpenBabel, plus FASTA/FASTQ sequence tools
- Everything runs on our server — nothing to install
- Works on desktop and mobile browsers