Find Similar Compounds
Build a compound library of chemically similar analogs by searching the PubChem database.
Menu: Compounds → Create Library → Find Similar Compounds
Guided tour: Launch in MolModa
This plugin identifies PubChem-catalogued compounds that are structurally similar to compounds chosen from your project.
Where to find it
Dialog
Parameters
This process may take some time for multiple molecules. Check the Jobs panel to monitor progress.
| Parameter | Default | Description |
|---|---|---|
makemolinputparams |
— | — |
| PubChem compounds to retrieve | similar |
Choose what kinds of molecules to retrieve from PubChem. Stereochemistry (chirality and E/Z double-bond geometry) is ignored. |
| Similarity threshold | 95 |
Value between 0 and 100. A higher threshold finds more similar compounds (95 is very similar, 80 is moderately similar). |
| Maximum results | 100 |
Maximum number of compounds to retrieve from PubChem. |
| Generate 3D coordinates | best |
Choose how to generate 3D atomic coordinates. |