Cluster-based selection

Cluster-based approaches try to divide molecules into groups or clusters of similar molecules. During the clustering process the intracluster similarity is maximized and the similarity between the clusters is minimized. From the resulting clusters, sets of compounds can be obtained by selecting one or more representatives from each cluster [76, 121, 122]. 

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Since diversity is a collective property, its precise quantification requires a mathematical description of the distribution of the molecular collection in a chemical space. When a set of molecules are considered to be more diverse than another, the molecules in this set cover more chemical space and/or the molecules distribute more evenly in chemical space. Historically, diversity analysis is closely linked to compound selection and combinatorial library design. In reality, library design is also a selection process, selecting compounds from a virtual library before synthesis. There are three main categories of selection procedures for building a diverse set of compounds cluster-based selection, partition-based selection, and dissimilarity-based selection. 

The cluster-based selection procedure starts with classifying compounds into clusters of similar molecules with a clustering algorithm followed by selection of representative(s) from each cluster (24). On the other hand, the partition-based selection procedure partitions chemical space into cells by dividing values of each dimension into various intervals and selects representative... 

Dunbar J. B. (1997) Cluster-based selection. Perspect Drug Discov Des 7/8,51-63. 

Ed., Perspectives in Drug Discovery and Design, Vol. 7/8, Kluwer/ESCOM, Dordrecht, The Netherlands, 1997, pp. 51-63. Cluster-Based Selection. 

With the necessary theory and background now in place, we move on to examine how to use the descriptors. In addition to what follows, the reader may wish to consult a special issue of Perspectives in Drug Discovery and Design from a few years ago entitled Computational Tools for the Analysis of Molecular Diversity. it contains review articles covering many of the issues discussed below cluster-based selection, partition-based selection, and... 

J. B. Dunbar Perspea. Drug Discovery Des., 7/8, 51 (1997). Cluster-Based Selection. 

Ligand Simulation Periodic structure selection Cluster-based selection ... 

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