Tools · Cheminformatics & Structure

Fingerprint Similarity & Clustering

Find nearest neighbors, cluster, pick diverse subsets, or map a library with UMAP and Leiden clustering, from Morgan or MACCS fingerprints.

Updated October 6, 2026

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Prices, workflows, and method papers Open in the app

Fingerprint Similarity & Clustering works on the 2D fingerprints of up to 10,000 molecules. Choose what to do with task:

`task`	What you get	Needs a `query`?
`neighbors`	The library molecules most similar to your query, ranked by Tanimoto similarity	Yes
`butina`	Butina clusters (each molecule's cluster and whether it is the centroid)	No
`maxmin`	A diverse subset picked with the MaxMin algorithm, in pick order	No
`leiden`	A map of the library: PCA, a neighbor graph, Leiden clusters, and 2D UMAP coordinates	No

Use neighbors to find analogs of a hit, butina or leiden to see the chemotypes in a library, and maxmin to pick a representative subset for purchase or screening.

How it works

Molecules are encoded as Morgan fingerprints (radius 2, 2048 bits, the default) or MACCS keys with RDKit. leiden then runs Scanpy: PCA (n_pcs, default 50), a k-nearest-neighbor graph (n_neighbors, default 15), Leiden community detection (leiden_resolution, default 1.0; higher gives more, smaller clusters), and UMAP for the 2D layout, with a fixed random seed so results repeat. It runs on CPU.

Inputs

A list of SMILES (at least 3 that parse), and for neighbors a query molecule. Unparseable SMILES are listed as errors; the job fails only if too few valid molecules remain.

Outputs

results.csv: one row per library molecule with the task's columns: tanimoto for neighbors, cluster_id and is_centroid for Butina, pick_order for MaxMin, or cluster_id with umap_1 and umap_2 for Leiden.
manifest.csv: how each input was parsed.
A molecules set for chaining: the Butina centroids, the MaxMin picks, or one representative per Leiden cluster.

For 3D shape and pharmacophore similarity use 3D Shape Similarity; to group by core structure use Scaffold Analyzer. The Build a library from building blocks, filter it, then dock workflow uses a MaxMin pick to choose which compounds to dock.

Run it from the API

Submit with Submit a job and the job_type below. Price it first with Estimate job reservation cost: submitting reserves that amount from your wallet, and the charge settles at the actual runtime.