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J Chem Inf Model. 2013 Aug 26;53(8):1979-89. doi: 10.1021/ci400206h. Epub 2013 Jul 30.

SMIfp (SMILES fingerprint) chemical space for virtual screening and visualization of large databases of organic molecules.

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Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.


SMIfp (SMILES fingerprint) is defined here as a scalar fingerprint describing organic molecules by counting the occurrences of 34 different symbols in their SMILES strings, which creates a 34-dimensional chemical space. Ligand-based virtual screening using the city-block distance CBD(SMIfp) as similarity measure provides good AUC values and enrichment factors for recovering series of actives from the directory of useful decoys (DUD-E) and from ZINC. DrugBank, ChEMBL, ZINC, PubChem, GDB-11, GDB-13, and GDB-17 can be searched by CBD(SMIfp) using an online SMIfp-browser at Visualization of the SMIfp chemical space was performed by principal component analysis and color-coded maps of the (PC1, PC2)-planes, with interactive access to the molecules enabled by the Java application SMIfp-MAPPLET available from These maps spread molecules according to their fraction of aromatic atoms, size and polarity. SMIfp provides a new and relevant entry to explore the small molecule chemical space.

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