Skip to main content
SpringerLink
Log in

A global resource for computational chemistry

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

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

.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Notes

  1. Earlier implementations of a commercial server-based computation and database systems were described only in the form of abstracts.

  2. Earlier implementations of a commercial server-based computation and database systems were described only in the form of abstracts.

  3. The NCI database has been previously used for similar purposes, for example to evaluate a proposed bond charge correction model for charge distributions in small molecules.

References

  1. Beck B, Horn A, Carpenter JE, Clark T (1998) J Chem Inf Comp Sci 38:1214–1217

    CAS  Google Scholar 

  2. Beck B (2000) Abstracts of papers, 220th ACS National Meeting, Washington DC, USA, August 20–24, COMP-151

  3. Pear M, Berstein J, Li C, McDonald R (1996) Book of abstracts, 212th ACS National Meeting, Orlando, FL, August 25–29, CINF-028

  4. Brown RD, Guner OF, Hahn M, Li H (1998) Book of abstracts, 216th ACS National Meeting, Boston, August 23–27, CINF-051

  5. Richards WG (2002) Innovation: nature reviews drug discovery 1:551–555

    Article  CAS  Google Scholar 

  6. Hawick KA, Grove DA, Coddington PD, Buntine MA (2000) Int J Chem article 4

  7. Hela M, Yousef YA, Afeneh AT (2002) J Comp Chem 23:966–976

    Article  Google Scholar 

  8. Zhang Y, Glen RC, Murray-Rust P, Rzepa HS, Townsend JA (2004) Abstracts of papers, 227th ACS National Meeting, Anaheim, CA, USA, March 28–April 1, CINF-032

  9. Murray-Rust P, Rzepa HS, Zhang Y (2004) Org Biomol Chem 2:3192–3203

    Article  PubMed  CAS  Google Scholar 

  10. Murray-Rust P, Rzepa HS, Williamson MJ, Willighagen EL (2004) J Chem Inf Comp Sci 44:462–469

    Article  CAS  Google Scholar 

  11. Jakalian A, Jack D, Bayly CI (2000) Abstracts of papers. Am Chem Soc COMP-001

  12. Stewart JJP (2004) Abstracts of papers. Am Chem Soc, COMP-004

  13. Murray-Rust P, Rzepa HS (1999) J Chem Inf Comp Sci 39:928–942

    Article  CAS  Google Scholar 

  14. Murray-Rust P, Rzepa HS (2003) J Chem Inf Comp Sci 43:757–772

    Article  CAS  Google Scholar 

  15. Sadowski J, Gasteiger J (1993) Chem Rev 93:2567–2581

    Article  CAS  Google Scholar 

  16. Linstrom PJ, Tchekhovskoi DV (2003) Abstracts of papers. Am Chem Soc, CINF-085

  17. Stein SE, Heller SR, Tchekhovski D (2003) Nimes International Chemical Information Conference Proceedings, pp 131–143

  18. Clark T, Martin S, Liefeld T (2004) Brief Bioinform 5:59–70

    Article  PubMed  CAS  Google Scholar 

  19. Godden JW, Stahura FL, Bajorath J (2000) J Chem Inf Comp Sci 40:796–800

    Article  CAS  Google Scholar 

  20. See http://www.w3c.org/Style/XSL/

  21. Tannenbaum T, Wright D, Miller K, Livny M (2002) Condor—a distributed job scheduler. In: Sterling T (ed) Beowulf cluster computing with linux. MIT Press, Cambridge, MA

  22. Thain D, Tannenbaum T, and Livny M (2003) “Condor and the grid”. In: Fran B, Anthony JGH, Geoffrey F (eds) Grid computing: making the global infrastructure a reality. Wiley, New York

    Google Scholar 

  23. See http://xml.apache.org/xindice/

  24. For details of CMLComp and other evolving schemas, see http://cml.sourceforge.net/

  25. Frey JG (2004) Abstracts of papers, 227th ACS National Meeting, CINF-025

  26. Hughes G, Mills H, De Roure D, Frey JG, Moreau L, Schraefel MC, Smith G, Zaluska E (2004) Org Biomol Chem 2:3284–3293

    Article  PubMed  CAS  Google Scholar 

  27. Berners-Lee T, Hendler J (2001) Nature 410:1023–1024

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK

    Peter Murray-Rust & Yong Zhang

  2. Department of Chemistry, Imperial College, London, SW7 2AY, UK

    Henry S. Rzepa

  3. Stewart Computational Chemistry, Colorado springs, CO, USA

    James J. P. Stewart

Authors
  1. Peter Murray-Rust
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Henry S. Rzepa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. James J. P. Stewart
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Henry S. Rzepa.

Electronic Supplementary Material

A list of molecules in the NCI database, encoded in CML (Chemical Markup Language), for which the computed InChI identifier differs before and after optimization using the MOPAC PM5 procedure.

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

Rights and permissions

Reprints and permissions

About this article

Cite this article

Murray-Rust, P., Rzepa, H.S., Stewart, J.J.P. et al. A global resource for computational chemistry. J Mol Model 11, 532–541 (2005). https://doi.org/10.1007/s00894-005-0278-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-005-0278-1

Keywords

Search

Navigation