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J Comput Aided Mol Des. 2011 Jul;25(7):611-20. doi: 10.1007/s10822-011-9461-x. Epub 2011 Jul 27.

Design of a fragment library that maximally represents available chemical space.

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  • 1YSBL, Chemistry Department, University of York, Heslington, York, YO10 5DD, UK.


Cheminformatics protocols have been developed and assessed that identify a small set of fragments which can represent the compounds in a chemical library for use in fragment-based ligand discovery. Six different methods have been implemented and tested on Input Libraries of compounds from three suppliers. The resulting Fragment Sets have been characterised on the basis of computed physico-chemical properties and their similarity to the Input Libraries. A method that iteratively identifies fragments with the maximum number of similar compounds in the Input Library (Nearest Neighbours) produces the most diverse library. This approach could increase the success of experimental ligand discovery projects, by providing fragments that can be progressed rapidly to larger compounds through access to available similar compounds (known as SAR by Catalog).

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