SAR analysis

Structure-Activity Relationship (SAR) analysis examines how changes in a molecule’s chemical structure affect its biological activity. OpenDDE provides two key SAR tools: the SAR scatter plot and activity cliff detection.

SAR scatter plot

The SAR plot visualizes all known ligands for a target on a 2D chart:

• X-axis: Molecular weight (Da)
• Y-axis: Activity (nM, log scale)
• Color: Clinical phase (if applicable)
• Size: LogP value

This visualization helps you quickly identify the “sweet spot” — compounds that are both potent (low nM) and drug-like (moderate MW).

Activity cliffs

An activity cliff is a pair of molecules that are:

• Structurally similar (Tanimoto similarity > 0.7 on Morgan fingerprints)
• Biologically different (activity ratio > 10×)

These are valuable because they reveal which small structural modifications cause the biggest changes in potency. OpenDDE automatically detects and ranks activity cliffs, showing side-by-side comparisons of each pair.

How cliffs are computed

1. All ligands with valid SMILES and activity data are collected (capped at 30)
2. Pairwise Tanimoto similarity is computed using Morgan fingerprints (radius 2)
3. Pairs with similarity > 0.7 and activity ratio > 10× are flagged
4. Top 10 cliffs are returned, sorted by activity ratio

Interpreting results

Next: System architecture →