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J Chem Inf Comput Sci. 2000 Jan;40(1):155-62.

Comparison of 2D fingerprint types and hierarchy level selection methods for structural grouping using Ward's clustering

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  • 1Parke-Davis Pharmaceutical Research Division, Warner-Lambert Company, Ann Arbor, Michigan 48105, USA.


Four different two-dimensional fingerprint types (MACCS, Unity, BCI, and Daylight) and nine methods of selecting optimal cluster levels from the output of a hierarchical clustering algorithm were evaluated for their ability to select clusters that represent chemical series present in some typical examples of chemical compound data sets. The methods were evaluated using a Ward's clustering algorithm on subsets of the publicly available National Cancer Institute HIV data set, as well as with compounds from our corporate data set. We make a number of observations and recommendations about the choice of fingerprint type and cluster level selection methods for use in this type of clustering

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