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We recently analyzed a large compound collection in 100
parallel protein-binding assays (48) and found both proteinbinding
frequencies and specificities are increased among compounds
having intermediate stereochemical complexity. Here,we extend analysis of the same compounds to physicochemical
properties (6, 7, 16, 54) and shape-based descriptors (27, 29),
revealing additional similarities and differences between sets.
We use principal component analysis (PCA) (55) of chemically
intuitive properties to analyze sources of variation among the
sets. Different descriptors report different aspects of chemical
structure (36), and we aim to illustrate for synthetic chemists
how quantitative relationships can be reconciled with chemical
intuition.

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