Journal of Computer-Aided Molecular Design

, Volume 10, Issue 3, pp 255–262 | Cite as

PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules

  • D. M. F. van Aalten
  • R. Bywater
  • J. B. C. Findlay
  • M. Hendlich
  • R. W. W. Hooft
  • G. Vriend
Research Paper


A software package is described that operates on small molecules observed in the PDB collection of protein structures. Molecular topology files for many molecular modeling programs can be generated automatically. The three-dimensional coordinates of small molecules can be converted to molecular descriptor strings that encode them uniquely in order to enable small-molecule recognition, despite high variability in atom and molecule nomenclature. From this descriptor a plausible 3D structure can be regenerated using energy minimisation. Alternatively, an ensemble of structures can be generated using a distance-geometry-based algorithm.


Molecular dynamics Graph theory SMILES 


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Copyright information

© ESCOM Science Publishers B.V 1996

Authors and Affiliations

  • D. M. F. van Aalten
    • 1
  • R. Bywater
    • 2
  • J. B. C. Findlay
    • 1
  • M. Hendlich
    • 3
  • R. W. W. Hooft
    • 4
  • G. Vriend
    • 4
  1. 1.Department of Biochemistry and Molecular BiologyUniversity of LeedsLeedsUK
  2. 2.Biostructure DepartmentNOVO NORDISK A/SBagsvaerdDenmark
  3. 3.Preclinical Research/Drug DesignMerck KGaADarmstadtGermany
  4. 4.BiocomputingEMBLHeidelbergGermany

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