Journal of Computer-Aided Molecular Design

, Volume 25, Issue 7, pp 611-620

First online:

Design of a Fragment Library that maximally represents available chemical space

  • M. N. SchulzAffiliated withYSBL, Chemistry Department, University of York
  • , J. LandströmAffiliated withYSBL, Chemistry Department, University of York
  • , K. BrightAffiliated withYSBL, Chemistry Department, University of York
  • , R. E. HubbardAffiliated withYSBL, Chemistry Department, University of YorkHYMS, University of YorkVernalis (R&D) Ltd Email author 

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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).


Fragment-based ligand discovery Library design SAR by catalog Nearest neighbours