Three-Dimensional Moments of Molecular Property Fields

Journal of Chemical Information and Computer Sciences

Volumn 40, Issue 6, 2000, Pages 1470-1476

  Silverman, B David ^a  

^a IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0011983262     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci000457s     Document Type: Article

References (38)

1. Hansch, C.; Leo, A. Exploring QSAR Fundamentals and Applications in Chemistry and Biology; American Chemical Society: Washington, DC, 1995.
2. Topological Indices and Related Descriptors in QSAR and QSPR; Devillers, J., Balaban, A. T., Eds.; Gordon and Breach: Amsterdam, 1999.
3. Cramer, R. D. III; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
4. Kellogg, G. E.; Semus, S. F.; Abraham, D. J. HINT: A new method of empirical hydrophobic field calculation for CoMFA. J. Comput-Aided Mol. Des. 1991, 5, 545-552.
5. Baroni, M.; Constantino, G.; Cruciani, G.; Riganelli, D.; Valigi, R.; Clementi, S. Generating optimal linear PLS estimations (GOLPE): an advanced chemornetric tool for handling 3DQSAR problems. Quant. Struct.-Act. Relat. 1993, 12, 9-20.
6. Kier, L. B.; Hall, L. H. In Molecular Structure Description, The Electrotopological State; Academic Press: San Diego, 1999; Chapter 4, p 62.
7. Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 1985, 28, 849-857.
8. Todeschini, R.; Gramatica, P. New 3D Molecular Descriptors: The Whim theory and QSAR Applications. In 3D QSAR in Drug Design; Kubinyi, H., Folkers, Martin, Y. C., Eds.; Kluwer/Escom: Dordrecht, 1998; Vol. 2, Part 3, p 355.
9. Gancia, E.; Bravi, G.; Mascagni, P.; Zaliani, A. Global 3D-QSAR methods: MS-WHIM and autocorrelation. J. Comput-Aided Mol. Des. 2000, 14, 293-306.
10. Pitman, M. C.; Huber, W. K.; Horn, H. H.; Rice, J. E.; Swope, W. C. FLASHFLOOD: A 3D Field-Based Similarity Search Method for Databases of Flexible Molecules. Submitted for publication.
11. Turner, D. B.; Willett, P. Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA). J. Comput-Aided Mol. Des. 2000, 14, 1-21.
12. Bursi, R.; Dao, T.; van Wijk, T.; de Gooyer, M.; Kellenbach, E.; Verwer, P. Comparative Spectra Analysis (CoSA): Spectra as Three-Dimensional Molecular Descriptors for the Prediction of Biological Activities. J. Chem. Inf. Comput. Sci. 1999, 39, 861-867.
13. Good, A. C.; So, S.-S.; Richards, W. G. Structure-Activity Relationships from Molecular Similarity Matrixes. J. Med. Chem. 1993, 36, 433-438.
14. Robert, D.; Amat, L.; Carbo-Dorca. Three-Dimensional Quantitative Structure-Activity Relationships from Tuned Molecular Quantum Similarity Measures: Prediction of the Corticosteroid-Binding Globulin Binding Affinity for a Steroid Family. J. Chem. Inf. Comput. Sci 1999, 39, 333-334.
15. Silverman, B. D.; Platt, D. E. Comparative Molecular Moment Analysis (CoMMA): 3D-QSAR without Molecular Superposition. J. Med. Chem. 1996, 39, 2129-2140.
16. Further details of the procedure are provided on the Web site http:// www.research.ibm.com/comma.
17. Eisenberg, D.; Weiss, R. M.; Terwilleger, T. C. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature 1982, 299, 371-374.
18. Ghose, A. K.; Crippen, G. M. Atomic Physicochemical Parameters for Three-Dimensional Structure-Directed Quantitative Structure-Activity Relationships I. Partition Coefficients as a Measure of Hydrophobicity. J. Comput. Chem. 1986, 7, 565-577.
19. Herman, R. M. Center of Dispersion Force in HCL Interacting with Rare-Gas Atoms. J. Chem. Phys. 1966, 44, 1346-1352.
20. Vegh, L. Scattering correlation in double ionization of helium by fast antiprotons and protons. Phys. Rev. A 1988, 37, 992-994.
21. Schmelcher, P.; Cederbaum, L. S. Approximate constant of motion for molecular ions in a magnetic field. Phys. Rev. A 1989, 40, 3515-3523.
22. Berant, Z.; Shahal, O.; Karpas, Z. Correlation between Measured and Calculated Mobilities of Ions: Sensitivity Analysis of the Fitting Procedure. J. Phys. Chem. 1991, 95, 7534-7538.
23. Dhuicq, D.; Jugi, B.; Benoit, C.; Sidis, V. The He++H-2>HeH++H*-(2s, 2p) reaction: Study of the s and p contributions in a coincidence-correlation experiment. J. Chem. Phys. 1998, 109, 1998.
24. Metral, C. J.; Janini, G. M.; Muschik, G. M.; Issaq, H. J. A Computer method for predicting the electiophoretic mobility of peptides. HRC-J. High-Resolut. Chromatogr. 1999, 22, 373-378.
25. Taubin, G.; Bolle, R. M.; Cooper, D. B. Representing and Comparing Shapes Using Shape Polynomials. IEEE Conference on Computer Vision and Pattern Recognition CVPR'89; 1989; pp 510-516.
26. Duda, R. O.; Hart, P. E. Pattern Classification and Scene Analysis; Wiley: New York, 1973; Chapter 9, p 364.
27. Wagener, M.; Sadowski, J.; Gasteiger, J. Autocorrelation of Molecular Surface Properties for Modeling Corticosteroid Binding Globulin and Cystolic Ah Receptor Activity by Neural Networks. J. Am. Chem. Soc. 1995, 117, 7769-7775.
28. Clementi, S.; Cruciani, G.; Riganelli, D.; Valigi, R.; Constantino, G.; Baroni, M.; Wold, S. Autocorrelation as a tool for a congruent description of molecules in 3D-QSAR studies. Pharm. Pharmacal. Lett. 1993, 3, 5-8.
29. Waller, C. L.; McKinney, J. D. Comparative Molecular Field Analysis of Polyhalogenated Dibenzo-p-dioxins, Dibenzofurans, and Biphenyls. J. Med. Chem. 1992, 35, 3660-3666.
30. A detailed review of this work is presented in: Safe, S. Polychloriniated Biphenyls (PCBs), Dibenzo-p-Dioxins (PCDDs), and Related Compounds: Environmental and Mechanistic Considerations Which Support the Development of Toxic Equivalency Factors (TEFs). Crit. Rev. Toxicol. 1990, 21, 51-88.
31. A brief historical review in a recent paper surveying molecular characterization can be found in: Livingstone, D. J. The Characterization of Chemical Structures Using Molecular Properties. A Survey. J. Chem. Inf. Comput. Sci. 2000, 40, 195-209.
32. Abraham, D. J. Kellog, G. E. Hydrophobic Fields in 3D QSAR in Drug Design, Theory, Methods, and Applications; Kubinyi, H., Ed.; Escom: Leiden, 1993; Part III. 3D QSAR Models, p 506.
33. Clark, M.; Cramer, R. D. III; Van Opdenbosch, N. Validation of the Tripos 5.2 Force Field. J. Comput. Chem. 1989, 10, 982-1012.
34. Matlab. The Mathworks Inc., 24 Prime Park Way, Natick, MA 01760.
35. Matlab Statistics Toolbox, The Mathworks Inc., 24 Prime Park Way, Natick, MA 01760.
36. Silverman, B. D. The Thirty-one Benchmark Steroids Revisited: Comparative Molecular Moment Analysis (CoMMA) with Principal Component Regression. Quant. Struct.-Act. Relat. 2000, 19, 237-246.
37. SYBYL: Available from TRIPOS Inc., 1699 S. Hanley Road, St. Louis, MO 63144.
38. The property-field center is actually a generalization of what has been called the "barycenter" (see, for example, http://spaceplace.jpl.nasa.gov/barycntr.htm).