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Using inverted indices for accelerating LINGO calculations.

Thomas G Kristensen1, Jesper Nielsen, Christian N S Pedersen

  • 1Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark. tgk@birc.au.dk

Journal of Chemical Information and Modeling
|February 22, 2011
PubMed
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Novel LINGO representation speeds up molecule comparison. This method, using sparse fingerprints and inverted indices, accelerates LINGOsim calculations 2.6x faster than previous techniques without specialized hardware.

Area of Science:

  • Computational Chemistry
  • Cheminformatics
  • Bioinformatics

Background:

  • Growing chemical databases necessitate efficient molecular representation and comparison methods.
  • LINGO fragmentation of SMILES strings offers a way to represent molecules.
  • LINGOsim, based on the Tanimoto coefficient, is used for comparing LINGO multisets.

Purpose of the Study:

  • To introduce a verbose representation for LINGO multisets.
  • To enable transformation of LINGO multisets into sparse fingerprints for accelerated queries.
  • To improve the speed of LINGOsim similarity matrix calculation.

Main Methods:

  • Developed a verbose representation for storing LINGO multisets.
  • Transformed verbose representations into sparse fingerprints.

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  • Utilized inverted indices for efficient similarity calculations.
  • Compared performance against previous hardware-dependent methods.

    • Main Results:

    • The new method allows LINGO multisets to be converted into sparse fingerprints.
    • Calculated LINGOsim similarity matrices approximately 2.6 times faster than existing methods.
    • Achieved significant speedup without requiring specialized hardware.

    Conclusions:

    • The verbose representation and inverted indices offer a hardware-independent acceleration for LINGOsim calculations.
    • This approach enhances the efficiency of molecular comparison in large chemical databases.
    • Provides a practical solution for accelerating cheminformatics queries.