Partition-based selection

Mason JS, Pickett, SD. Partition-based selection. Perspect Drug Discov Des, 1997 7/8 85-114. 

Mason, J.S. and Pickett, S.D. Partition-based selection. Perspect. Drug Disc. Des. 1997, 7/8, 85-114. 

Many of the early evaluations of the effectiveness of diversity methods used structure-based diversity indices, such as functions of intermolecular dissimilarities in the context of distance-based selection methods or of the numbers of occupied cells in partition-based selection methods (4). A wide range of such indices has been reported, as discussed in the excellent review by Waldman et al. 

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... 

The principal factor to be considered in partition-based selection is the set of characteristics that is used to define the chemical space. The first report of such an approach was by Mason et al. [58], who generated partitions defined by six global molecular properties that had been chosen to... 

Diversity, P. Willett, Ed., Perspectives in Drug Discovery and Design, Vol. 7/8, Kluwer/ ESCOM, Dordrecht, The Netherlands, 1997, pp. 85-114. Partition-Based Selection. 

Partition-based selection is much faster than clustering, mapping, or dissimilarity methods because no similarities of pairs of molecules have to be calculated. 

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... 

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