A browser-based tool for aligning molecular structures to a common reference scaffold and highlighting the differences. It runs entirely in your browser using RDKit.js (WebAssembly) – no installation required.

How to use

  1. Prepare a SMILES file (tab-separated: SMILES, Catalog ID, and any additional properties) or an SDF file with your molecules.
  2. Enter a reference SMILES representing the common scaffold you want to align against.
  3. Click Load & Align. The tool will find the maximum common substructure (MCS) between the reference and each molecule, align their 2D coordinates, and highlight atoms that differ from the reference in green.

Features

  • Interactive highlighting – toggle Edit Highlights mode and click individual atoms to add or remove highlights.
  • Rotation & mirroring – adjust the orientation of any selected molecule while keeping atom labels upright.
  • Atom selector dialog – bulk select/deselect atoms for highlighting via checkboxes.
  • Configurable labels – choose font size and which molecular property to display as a second line (e.g., price, MW).
  • High-resolution PNG export – export the entire grid at 2x resolution for publications or presentations.