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Fragment Database FDB-17.

Ricardo Visini1, Mahendra Awale1, Jean-Louis Reymond1

  • 1Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Berne, Switzerland.

Journal of Chemical Information and Modeling
|April 5, 2017
PubMed
Summary

A new fragment database, FDB-17, offers 10 million diverse, small molecules for drug discovery. This subset of GDB-17 aids in selecting novel fragment-sized molecules for synthesis.

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Area of Science:

  • Computational chemistry and cheminformatics.
  • Drug discovery and molecular design.

Background:

  • The GDB-17 database contains 166.4 billion molecules, offering a vast chemical space.
  • GDB-17 is biased towards large, complex molecules, limiting its utility for virtual screening.

Purpose of the Study:

  • To create a smaller, more manageable subset of GDB-17 for broader accessibility.
  • To facilitate the selection of fragment-sized molecules for chemical synthesis and drug discovery.

Main Methods:

  • Systematic enumeration of molecules up to 17 atoms (C, N, O, S, halogen).
  • Selection of a subset (FDB-17) focusing on fragment-like properties.
  • Development of an interactive visualization and nearest neighbor search tool.

Main Results:

  • FDB-17 comprises 10 million fragment-like molecules.
  • FDB-17 evenly covers molecular size, polarity, and stereochemical complexity.
  • The database is available for free download with search and visualization tools.

Conclusions:

  • FDB-17 provides a valuable resource for exploring fragment-sized chemical space.
  • The database and associated tools simplify the identification of novel molecules for synthesis.

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