Journal of Computer-Aided Molecular Design

, Volume 10, Issue 6, pp 607–622 | Cite as

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

  • J. E. J. Mills
  • P. M. Dean
Research Papers


An extensive crystal survey of the Cambridge Structural Database has been carried out to provide hydrogen-bond data for use in drug-design strategies. Previous crystal surveys have generated 1D frequency distributions of hydrogen-bond distances and angles, which are not sufficient to model the hydrogen bond as a ligand-receptor interaction. For each hydrogen-bonding group of interest to the drug designer, geometric hydrogen-bond criteria have been derived. The 3D distribution of complementary atoms about each hydrogen-bonding group has been ascertained by dividing the space about each group into bins of equal volume and counting the number of observed hydrogen-bonding contacts in each bin. Finally, the propensity of each group to form a hydrogen bond has been calculated. Together, these data can be used to predict the potential site points with which a ligand could interact and there-fore could be used in molecular-similarity studies, pharmacophore query searching of databases, or de novo design algorithms.


Ligand-receptor interaction Geometry of intermolecular interactions Cambridge Structural Database Drug design 


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Copyright information

© ESCOM Science Publishers B.V 1996

Authors and Affiliations

  • J. E. J. Mills
    • 1
  • P. M. Dean
    • 1
  1. 1.Drug Design Group, Department of PharmacologyUniversity of CambridgeCambridgeU.K.

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