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

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

  • Schwartz J Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.
  • Awale M
  • Reymond JL
  • 2013-07-13
Published in:
  • Journal of chemical information and modeling. - 2013
Databases, Pharmaceutical
Drug Evaluation, Preclinical
Informatics
Internet
Ligands
Organic Chemicals
User-Computer Interface
English 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.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://sonar.ch/global/documents/268208
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