Journal of Computer-Aided Molecular Design

, 25:611

Design of a Fragment Library that maximally represents available chemical space


  • M. N. Schulz
    • YSBL, Chemistry DepartmentUniversity of York
  • J. Landström
    • YSBL, Chemistry DepartmentUniversity of York
  • K. Bright
    • YSBL, Chemistry DepartmentUniversity of York
    • YSBL, Chemistry DepartmentUniversity of York
    • HYMS, University of York
    • Vernalis (R&D) Ltd

DOI: 10.1007/s10822-011-9461-x

Cite this article as:
Schulz, M.N., Landström, J., Bright, K. et al. J Comput Aided Mol Des (2011) 25: 611. doi:10.1007/s10822-011-9461-x


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 discoveryLibrary designSAR by catalogNearest neighbours

Supplementary material

10822_2011_9461_MOESM1_ESM.doc (318 kb)
Supplementary material 1 (DOC 318 kb)

Copyright information

© Springer Science+Business Media B.V. 2011