Similarity Measures

• Many ways of computing the similarity between two molecules

  • Different representations
  • Different similarity coefficients
  • Different weighting schemes

• Representations

  • Fingerprints (both 2D and 3D)
  • Connection tables (both 2D and 3D)
  • Physicochemical property vectors (“dataprints”)

• Database searching normally uses 2D fingerprints with the Tanimoto Coefficient

  • Seems to work reasonably well, in terms of both efficiency and effectiveness

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