PubChem Similarity Search
Find structurally similar compounds in PubChem from SMILES, SDF, or CCD queries.
Overview
Search the PubChem database for compounds that are structurally similar to one or more query molecules. Query molecules can be supplied as SMILES, SDF, or CCD codes, and results are returned as a ranked table with compound identifiers, names, formulas, molecular weights, and similarity scores.
Run PubChem Similarity Search on Neurosnap
The PubChem Similarity Search online webserver allows anybody with a Neurosnap account to run and access PubChem Similarity Search, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- Runs a 2D structural similarity search against PubChem for one or more query molecules.
- Accepts SMILES, SDF, and CCD query molecules so results can feed directly from other tools.
- Returns ranked compounds with CIDs, names, molecular formulas, molecular weights, and similarity scores.
- Bundles matched compound structures as SDF records for downstream modeling and screening.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access PubChem Similarity Search using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using PubChem Similarity Search in publications or research outputs.
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Kim S, Chen J, Cheng T, et al. PubChem 2025 update. Nucleic Acids Research. 2025;53(D1):D1512-D1525. https://doi.org/10.1093/nar/gkae1059 |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |