MolDraw Docs

Compare Molecules plugin

Short answer: Install Compare molecules, open the Compare tab, press Add canvas for the reference, paste other SMILES and press Add SMILES.

Last updated · By the MolDraw team at LabCanvas

View .mdSection PDF
MolDraw Compare molecules plugin comparing chloramphenicol with salicylic acid and paracetamol, showing structure and functional similarity percentages
Chloramphenicol as the reference, next to salicylic acid and paracetamol. You see two similarity scores and a list of changes.
  1. Compare tab.
  2. Add canvas adds the current drawing (the first molecule is the reference).
  3. SMILES box: one SMILES per line, optional name after a space.
  4. Add SMILES adds them all to the table.
  5. CSV exports the comparison table.

What it does#

Pick one molecule as the reference. Add others to compare.

  • Structure similarity is a Tanimoto score from fingerprints.
  • Functional similarity compares the groups each molecule has.
  • Changes lists groups gained, lost or changed.
  • Export the table as CSV.

Who it is for#

Medicinal chemists who look at analogues. Students who compare isomers or drug series.

How to use it#

  1. Open the MolDraw editor and sign in. Click Settings, then Plugins, then Install next to Compare Molecules.
  2. Draw the reference molecule.
  3. Open the Compare tab (callout 1) and press Add canvas (callout 2).
  4. Paste more structures as SMILES, one per line (callout 3), then press Add SMILES (callout 4).
  5. Click a row to see reference and selected structures side by side with the shared core highlighted.
  6. Sort by similarity, and press CSV (callout 5) to export.

Tips#

  • Tanimoto 1.00 can still hide stereo differences; check the stereo flag column.
  • Use the ChEMBL plugin's Send to Compare to add database hits directly.
  • To get SMILES, convert names with name to SMILES.

Questions and answers

What is Tanimoto similarity?

The number of fingerprint bits two molecules share divided by the number set in either. 1 means identical fingerprints; above about 0.7 is usually considered similar.

How many molecules can I compare?

You can add many rows at once by pasting a list of SMILES; the first molecule added is the reference.

Does it detect stereoisomers?

Yes, stereocentre differences are reported separately because fingerprints ignore stereochemistry.