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Related Experiment Videos

Similarity by compression.

James L Melville1, Jenna F Riley, Jonathan D Hirst

  • 1School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.

Journal of Chemical Information and Modeling
|January 24, 2007
PubMed
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We developed a straightforward method for molecular similarity searching using data compression. This approach, based on normalized compression distance, outperforms traditional methods in virtual high-throughput screening.

Area of Science:

  • Computational chemistry
  • Bioinformatics
  • Cheminformatics

Background:

  • Virtual high-throughput screening (vHTS) is crucial for drug discovery.
  • Current similarity searching methods often require complex data structures and algorithms.
  • There is a need for simpler, more efficient similarity searching techniques.

Purpose of the Study:

  • To introduce a novel, simple, and effective method for similarity searching in vHTS.
  • To demonstrate the utility of normalized compression distance (NCD) for molecular similarity.
  • To compare the performance of NCD-based searching against established methods.

Main Methods:

  • Utilizing string-based molecular representations (e.g., SMILES).
  • Employing standard data compression software.

Related Experiment Videos

  • Calculating normalized compression distance (NCD) as a measure of similarity, approximating normalized information distance and Kolmogorov complexity.

    • Main Results:

    • Compression-based similarity searching demonstrated superior performance compared to standard protocols.
    • The Tanimoto coefficient with binary fingerprints and data fusion was outperformed.
    • The method is computationally inexpensive and requires only basic software.

    Conclusions:

    • Normalized compression distance offers a powerful and accessible approach for molecular similarity searching.
    • This method provides a viable and potentially superior alternative for virtual high-throughput screening.
    • The simplicity and effectiveness of this technique facilitate broader application in drug discovery.