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How is chemical diversity assessed?

Tuesday, 29 September 2009 19:58
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Ed Champness

Chemical diversity can be defined in terms of the chemical structure and/or compound properties. For the chemical structure it is defined in terms of the patterns of atoms present in their chemical structures. The patterns of atoms along ‘paths’ through the 2D chemical structure of a compound are encoded in a binary ‘fingerprint’ and the similarity of two compounds is defined by a Tanimoto coefficient. The advantage of a path-based fingerprint approach to similarity and diversity is that it provides a ‘generic’ method of comparing compounds. For properties it is defined in terms of Euclidean distance between two points - the smaller the distance, the greater the similarity. A diverse set of compounds is determined by one of three metrics:

  • Maximin - the minimum distance between any two chosen compounds is maximised
  • S-optimal - the harmonic mean distance between pairs of chosen compounds is optimised so that they are spread out
  • Max Average - the average distance between all chosen compounds is maximised

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