Journal of Molecular Modeling

, Volume 11, Issue 6, pp 532–541 | Cite as

A global resource for computational chemistry

  • Peter Murray-Rust
  • Henry S. Rzepa
  • James J. P. Stewart
  • Yong Zhang
Original Paper


A modular distributable system has been built for high-throughput computation of molecular structures and properties. It has been used to process 250,000 compounds from the NCI database and to make the results searchable by structures and properties. The IUPAC/NIST InChI specification and algorithm has been used to index the structures and enforce integrity during computation. A number of novel features of the PM5 Hamiltonian were identified as a result of the high-throughput approach. The system and the data can be redistributed and reused and promote the value of computed data as a primary chemical resource

Figure Workflow schematic for conversion of an SDF file to a Mopac input file



Workflow InChI NCI Mopac XML-CML 

Supplementary material (2.9 mb)
List of molecules in the NCI database (zip-file 3,1 MB)


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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Peter Murray-Rust
    • 1
  • Henry S. Rzepa
    • 2
  • James J. P. Stewart
    • 3
  • Yong Zhang
    • 1
  1. 1.Department of ChemistryUnilever Centre for Molecular Informatics, University of CambridgeCambridgeUK
  2. 2.Department of ChemistryImperial CollegeLondonUK
  3. 3.Stewart Computational ChemistryColorado springsUSA

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