Skip to main content

A Novel Approach to QSPR/QSAR Based on Neural Networks for Structures

  • Chapter
Soft Computing Approaches in Chemistry

Part of the book series: Studies in Fuzziness and Soft Computing ((STUDFUZZ,volume 120))

Abstract

We present a novel approach based on neural networks for structures to QSPR (quantitative structure-property relationships) and QSAR (quantitative structure-activity relationships) analysis. We face two quite different chemical applications using the same model, i.e. predicting the boiling point of a class of alkanes and QSAR of a class of benzodiazepines. The model, Cascade Correlation for structures, is a class of recursive neural networks recently proposed for the processing of structured domains. Through the use of this model we can represent and process the structure of chemical compounds in the form of labeled trees. We report our results on preliminary applications to show that the model, adopting this representation of molecular structure, can adaptively capture significant topological aspects and chemical fnnctionalities for each specific class of the molecules, just on the basis of the association between the molecular morphology and the target property.

Partially supported by MURST grant 9903244848 and MM09308497.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. C. Hansch, P.P. Maloney, T. Fujita, and R.M. Muir. Correlation of biological activity of phenoxyacetic acids with hammett substituent constants and partition coefficients. Nature, 194: 178–180, 1962.

    Article  Google Scholar 

  2. C Hansch and T. Fujita. Analysis. A method for the correlation of biological activity and chemical structure. J. Am. Chem. Soc., 86: 1616–1626, 1964.

    Article  Google Scholar 

  3. S.M. Free Jr. and J.W. Wilson. A mathematical contribution to structure-activity studies. J. Med. Chem., 7: 395–399, 1964.

    Article  Google Scholar 

  4. L. H. Hall and L. B. Kier. Reviews in Computational Chemistry, chapter 9, The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modeling, pp 367–422. VCH Publishers, Inc.: New York, 1991.

    Google Scholar 

  5. D. H. Rouvray. Should we have designs on topological indices? In R. B. King, editor, Chemical Applications of Topology and Graph Theory, pp 159–177. Elsevier Science Publishing Company, 1983.

    Google Scholar 

  6. V. R. Magnuson, D. K. Harris, and S. C. Basak. Topological indices based on neighborhood symmetry: Chemical and biological application. In R. B. King, editor, Chemical Applications of Topology and Graph Theory, pp 178–191. Elsevier Science Publishing Company, 1983.

    Google Scholar 

  7. M. Barysz, G. Jashari, R. S. Lall, V. K. Srivastava, and N. Trinajstic. On the distance matrix of molecules containing heteroatoms. In R. B. King, editor, Chemical Applications of Topology and Graph Theory, pp 222–230. Elsevier Science Publishing Company, 1983.

    Google Scholar 

  8. A. Sperduti and A. Starita. Supervised neural networks for the classification of structures. IEEE Trans on Neural Networks, 8 (3): 714–735, 1997.

    Article  Google Scholar 

  9. P. Frasconi, M. Gori, and A. Sperduti. A general framework for adaptive processing of data structures. In IEEE Trans on Neural Networks, 9: 768–785, 1998.

    Google Scholar 

  10. D. Hadjipavlou-Litina and C. Hansch. Quantitative Structure-Activity Relationships of the benzodiazepines. A review and reevaluation. Chemical Reviews, 94(6): 1483–1505, 1994.

    Article  Google Scholar 

  11. D. Cherqaoui and D. Villemin. Use of neural network to determine the boiling point of alkanes. J. Chem. Soc. Faraday Trans., 90 (1): 97–102, 1994.

    Article  Google Scholar 

  12. A.M. Bianucci, A. Micheli, A. Sperduti, and A. Starita. Quantitative structure-activity relationships of benzodiazepines by recursive cascade correlation. In IEEE International Joint Conference on Neural Networks, pp 117–122, 1998.

    Google Scholar 

  13. A.M. Bianucci, A. Micheli, A. Sperduti, and A. Starita. Application of cascade correlation networks for structures to chemistry. Journal of Applied Intelligence, 12: 117–147, 2000.

    Article  Google Scholar 

  14. A. Micheli, A. Sperduti, A. Starita, and A.M. Bianucci. Analysis of the internal representations developed by neural networks for structures applied to quantitative structure-activity relationship studies of benzodiazepines. Journal of Chemical Information and Computer Sciences, 41 (1): 202–218, January 2001.

    Google Scholar 

  15. Y. Suzuki T. Aoyama and H. Ichikawa. Neural networks applied to quantitative structure-activity relationships. J. Med. Chem., 33: 2583–2590, 1990.

    Article  Google Scholar 

  16. Ajay. A unified framework for using neural networks to build QSARs. J. Med. Chem., 36: 3565–3571, 1993.

    Article  Google Scholar 

  17. K. L. Peterson. Quantitative structure-activity relationships in carboquinones and benzodiazepines using counter-propagation neural networks. J. Chem. Inf. Comput. Sci., 35 (5): 896–904, 1995.

    Google Scholar 

  18. A. F. Duprat, T. Huynh, and G. Dreyfus. Towards a Principled Methodology for Neural Network Design and Performance Evaluation in QSAR; Application to the Prediction of LogP. J. Chem. Inf. Comput. Sci., pp 854–866, 1998.

    Google Scholar 

  19. Shuhui Liu, Ruisheng Zhang, Mancang Liu, and Zhide Hu. Neural networks-topological indices approach to the prediction of properties of alkene. J. Chem. Inf. Comput. Sci., 37: 1146–1151, 1997.

    Google Scholar 

  20. D. W. Elrod, G. M. Maggiora, and R. G. Trenary. Application of neural networks in chemistry. 1. prediction of electrophilic aromatic substitution reactions. J. Chem. Inf. Comput. Sci., 30: 447–484, 1990.

    Google Scholar 

  21. V. Kvasnitka and J. Pospichal. Application of neural networks in chemistry.prediction of product distribution of nitration in a series of monosubstituted benzenes. J. Mol. Struct. (Theochem), 235: 227–242, 1991.

    Article  Google Scholar 

  22. James Devillers, editor. Neural Networks in QSAR and Drug Design. Academic Press, London, 1996.

    Google Scholar 

  23. J. Zupan and J. Gasteiger. Neural Networks for Chemists: an introduction. VCH Publishers, NY(USA ), 1993.

    Google Scholar 

  24. J. A. Burns and G. M. Whitesides. Feed-forward neural networks in chemistry: Mathematical system for classification and pattern recognition. Chemical Reviews, 93 (8): 2583–2601, 1993.

    Article  Google Scholar 

  25. S. E. Fahlman and C. Lebiere. The cascade-correlation learning architecture. In D. S. Touretzky, editor, Advances in Neural Information Processing Systems 2, pp 524–532. San Mateo, CA: Morgan Kaufmann, 1990.

    Google Scholar 

  26. S. E. Fahlman. The recurrent cascade-correlation architecture. In R.P. Lippmann, J.E. Moody, and D.S. Touretzky, editors, Advances in Neural Information Processing Systems 3, pp 190–196, San Mateo, CA, 1991. Morgan Kaufmann Publishers.

    Google Scholar 

  27. A. Sperduti, D. Majidi, and A. Starita. Extended cascade-correlation for syntactic and structural pattern recognition. In Petra Perner, Patrick Wang, and Azriel Rosenfeld, editors, Advances in Structural and Syntactical Pattern Recognition, volume 1121 of Lecture notes in Computer Science, pp 90–99. Springer-Verlag, Berlin, 1996.

    Chapter  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Bianucci, A.M., Micheli, A., Sperduti, A., Starita, A. (2003). A Novel Approach to QSPR/QSAR Based on Neural Networks for Structures. In: Cartwright, H.M., Sztandera, L.M. (eds) Soft Computing Approaches in Chemistry. Studies in Fuzziness and Soft Computing, vol 120. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-36213-5_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-36213-5_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-53507-9

  • Online ISBN: 978-3-540-36213-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics