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A Primer on Molecular Similarity in QSAR and Virtual Screening
Part I - Descriptor Choice

References

  1. Crum Brown, A.; Frazer, T., Trans. Roy. Soc. Edinburgh 1868, 24, 151.
  2. Hansch, C.; Fujita, T., Rho-Sigma-Pi Analysis . Method for Correlation of Biological Activity + Chemical Structure. J. Am. Chem. Soc. 1964, 86, (8), 1616-&.
  3. Bender, A.; Glen, R. C., Molecular similarity: a key technique in molecular informatics. Org. Biomol. Chem. 2004, 2, (22), 3204-3218.
  4. Bender, A.; Jenkins, J. L.; Li, Q.; Adams, S. E.; Cannon, E. O.; Glen, R. C., Molecular Similarity: Advances in Methods, Applications, and Validations in Virtual Screening and QSAR. Annual Reports In Computational Chemistry 2006, 2, 141 - 168.
  5. Topliss, J. G.; Edwards, R. P., Chance factors in studies of quantitative structure-activity relationships. J. Med. Chem. 1979, 22, (10), 1238-44.
  6. Livingstone, D. J.; Salt, D. W., Judging the significance of multiple linear regression models. J Med Chem 2005, 48, (3), 661-3.
  7. Salt, D. W.; Ajmani, S.; Crichton, R.; Livingstone, D. J., An improved approximation to the estimation of the critical f values in best subset regression. J Chem Inf Model 2007, 47, (1), 143-9.
  8. Renner, S.; Schneider, G., Scaffold-hopping potential of ligand-based similarity concepts. ChemMedChem 2006, 1, (2), 181-5.
  9. Glen, R. C.; Bender, A.; Arnby, C. H.; Carlsson, L.; Boyer, S.; Smith, J., Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME. IDrugs 2006, 9, (3), 199-204.
  10. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A., Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org. Biomol. Chem. 2004, 2, (22), 3256-3266.
  11. Good, A. C.; Hermsmeier, M. A.; Hindle, S. A., Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments. J. Comput.-Aided Mol. Des. 2004, 18, (7), 529-536.
  12. SciTegic, I., San Diego, CA. - http://www.scitegic.com., SciTegic, Inc., San Diego, CA. - http://www.scitegic.com. In.
  13. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S., Molecular similarity searching using atom environments, information-based feature selection, and a naive bayesian classifier. J. Chem. Inf. Comput. Sci. 2004, 44, (1), 170-178.
  14. Bender, A.; Glen, R. C., A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication. J. Chem. Inf. Model. 2005, 45, (5), 1369-1375.
  15. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A., Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures. J. Chem. Inf. Comput. Sci. 2004, 44, (3), 1177-1185.
  16. Melville, J. L.; Riley, J. F.; Hirst, J. D., Similarity by compression. J Chem Inf Model 2007, 47, (1), 25-33.

 

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