title: SMIfp (SMILES fingerprint) chemical space for virtual screening and visualization of large databases of organic molecules.
abstract: 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 www.gdb.unibe.ch. 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 www.gdb.unibe.ch. 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.
authors.affiliation: Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.
authors.forename: Julian
authors.initials: J
authors.lastname: Schwartz
authors.forename: Mahendra
authors.initials: M
authors.lastname: Awale
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Reymond
mesh_terms: D062313:Databases, Pharmaceutical; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D048088:Informatics / Q000379:methods*; D020407:Internet; D008024:Ligands; D009930:Organic Chemicals / Q000737:chemistry*; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D009930:Organic Chemicals