CHEMPASS; A Tool for Chemical Structure Similarity Scoring and Clustering.

Upload your list of compounds in .csv/.txt format either as CID/DTXSIDs/SMILES, select your choice of fingerprint generation, set the clustering threshold, and explore cluster-level statistics and heatmaps.

zip file for download includes a .pdf of clusters with similarity scores, molecular properties of compounds, high resolution images of heatmap and NMDS plots.

Use example data to test the app without uploading a file.

Processing an arbitrary list of 15 CIDs provided as example data

Download example data
Upload File: [?]

Please upload a list of compounds in text (.txt) or CSV (.csv) format containing one or more of these identifiers.

  • CID: Compound Identification Number (PubChem). eg: 1983 (for Acetaminophen)
  • SMILES: Simplified Molecular Input Line Entry System, a line notation for describing the structure of chemical species. eg: CC(=O)NC1=CC=C(O)C=C1
  • DTXSID: DSSTox Substance Identifier used in the Environmental Protection Agency CompTox Dashboard. eg: DTXSID0020232
DTXSID5025659
DTXSID5025811
6950
8295
C(C(=O)NCC(=O)O)N
CC(=O)NCCCCN

Select fingerprint type: [?]

What are Morgan fingerprints?

Morgan fingerprints encode molecular structures by considering circular atom neighborhoods.

  • ECFP4: Focuses on atom and bond connectivity (radius 2).
  • FCFP4: Focuses on functional classes of atoms like donor/acceptor roles.

Clustering Cutoff: [?]

What does Clustering Cutoff mean?

This value sets the distance threshold.

• A lower cutoff (e.g., 0.2) forms tighter, smaller clusters.

• A higher cutoff (e.g., 0.6) forms larger, looser clusters.

Adjust the cutoff depending on how strict you want your clustering to be.

For chemical structure clustering, a cutoff of 0.2–0.4 is often a good starting point.

For smaller datasets with fewer than 20 compounds, you may need to increase the cutoff beyond 0.4

  • Heatmap
  • Butina Clusters
  • NMDS Plot
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