Outliers detection in the statistical accuracy test of a pKa prediction

Journal of Mathematical Chemistry

Volumn 47, Issue 2, 2010, Pages 891-909

  Meloun, Milan ^a   Bordovská, Sylva ^a   Kupka, Karel ^b  

^a UNIVERSITY OF PARDUBICE   (Czech Republic)

^b Statistical Software Ltd   (Czech Republic)

Author keywords

Dissociation constants; Goodness of fit; Outliers; PKa prediction; Residuals; Williams graph

Indexed keywords

EID: 77952955263     PISSN: 02599791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10910-009-9609-2     Document Type: Article

References (46)

1. Xing L., Glen R. C.: Novel methods for the prediction of log P, pK and log D. J. Chem. Inf. Comput. Sci. 42, 796-805 (2002).
2. a by molecular tree structured fingerprints and PLS. J. Chem. Inf. Comput. Sci. 43, 870-879 (2003).
3. a values for aliphatic carboxylicv acids and alcohols with empirical atomic charge descriptors. J. Chem. Inf. Model. 46, 2256-2266 (2006).
4. Hansen N. T., Kouskoumvekaki I., Jorgensen F. S., Brunak S., Jonsdottir S. O.: Prediction of pH-dependent aqueous solubility of druglike molecules. J. Chem. Inf. Model. 46, 2601-2609 (2006).
5. a Predictor 3.0, Advanced Chemistry Development Inc. 133 Richmond St. W. Suite 605, Toronto.
6. a) for 22 drugs. Quant. Struct. Act. Relat. 12, 152 (1993).
7. a with experimental values. Pharm. Sci. 83, 1280-1283 (1994).
8. a September 1998 predictions, (Poster), AAPS, Boston, November 1997.
9. a calculation module, QUANTUM pharmaceuticals, http://www.q-lead.com.
10. Z. Gulyás, G. Pöcze, A. Petz, F. Darvas, Pallas cluster-a new solution to accelerate the high-throughut ADME-TOX prediction, ComGenex-CompuDrug, PKALC/PALLAS 2.1 CompuDrug Chemistry Ltd., http://www. compudrug. com.
11. TM, http://www.CombiSep.com.
12. Evagelou V., Tsantili-Kakoulidou A., Koupparis M.: Determination of the dissociation constants of the cephalosporins cefepime and cefpirome using UV spectrometry and pH potentiometry. J. Pharm. Biomed. Anal. 31, 1119-1128 (2003).
13. a control of the retinal Schiff base: a density functional study. J. Phys. Chem. B 103, 4518-4527 (1999).
14. SYBYL is distributed by tripos, Inc., St. Louis MO 63144, http://www.tripos.com.
15. Marvin: http://www. chemaxon. com/conf/Prediction_of_dissociation_constant_using_microcon-stants. pdf and http://www. chemaxon. com/conf/New_method_for_pKa_estimation. pdf.
16. a values of hydroxybenzoic acids in aqueous solution with special reference to the hydrophobicity of hydroxybenzoates and their binding to surfactants. J. Phys. Chem. B 102, 1938-1944 (1998).
17. a of carboxylic acids using the ab initio Continuum-Solvation Model PCM-UAHF. J. Phys. Chem. A 102, 6707-6712 (1998).
18. a values in aqueous solution I. Carboxylic acids. J. Phys. Chem. A 103, 11194-11199 (1999).
19. Tran N. L., Colvin M. E.: The prediction of biochemical acid dissociation constants using first principles quantum chemical simulations. Theochem 532, 127-137 (2000).
20. a of phenols, carboxylic acids and alcohols from semiempirical quantum chemical methods. Chemosphere 38, 191-206 (1999).
21. a of pyridine using semiempirical and ab initio methods. Theor. Chem. Acc. 103, 483-494 (2000).
22. a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29, 10219-10225 (1990).
23. Oberoi H., Allewell N. M.: Multigrid solution of the nonlinear Poison-Boltzmann equation and calculation of titration curves. Biophys. J. 65, 48-55 (1993).
24. Antosiewicz J., McCammon J. A., Gilson M. K.: Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238, 415-436 (1994).
25. a's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J. Phys. Chem. B 101, 4458-4472 (1997).
26. Kim K. H., Martin Y. C.: Direct prediction of linear free energy substituent effects from 3D structures using comparative molecular field effect. 1. Electronic effect of substituted benzoic acids. J. Org. Chem. 56, 2723-2729 (1991).
27. Kim K. H., Martin Y. C.: Direct prediction of dissociation constants of clonidine-like imidazolines, 2-substituted imidazoles, and 1-methyl-2-substituted imidazoles from 3D structures using a comparative molecular field analysis (CoMFA) approach. J. med. Chem. 34, 2056-2060 (1991).
28. a prediction for nucleic acids components. J. Comput. Aided Mol. Des. 13, 611-623 (1999).
29. a prediction for organic acids and bases. Chapman and Hall Ltd., London (1981).
30. CompuDrug NA Inc., pKALC version 3.1, (1996).
31. a version 1.0, (1997).
32. http://chemsilico.com/CS_prpKa/PKAhome.html. Accessed Aug 2006.
33. Habibi-Yangjeh A., Danandeh-Jenagharad M., Nooshyar M.: Prediction acidity constant of various benzoic acids and phenols in water using linear and nonlinear QSPR models. Bull. Korean Chem. Soc. 26, 2007-2016 (2005).
34. Popelier P. L. A., Smith P. J.: QSAR models based on quantum topological molecular similarity. Eur. J. Med. Chem. 41, 862-873 (2006).
35. Schmid G. H. et al.: The application of iterative optimization techniques to chemical kinetic data of large random error. Can. J. Chem. 54, 3330-3341 (1976).
36. M. Meloun, J. Militký, M. Forina, Chemometrics for Analytical Chemistry, Vol. 2. PC-Aided Regression and Related Methods (Ellis Horwood, Chichester, 1994), and Vol. 1. PC-Aided Statistical Data Analysis (Ellis Horwood, Chichester, 1992).
37. S-PLUS: MathSoft, Data Analysis Products Division, 1700 Westlake Ave N, Suite 500, Seattle, WA 98109, USA, http://www.insightful.com/products/splus (1997).
38. ADSTAT: ADSTAT 1.25, 2.0, 3.0 (Windows 95), TriloByte Statistical Software Ltd., Pardubice, Czech Republic.
39. Belsey D. A., Kuh E., Welsch R. E.: Regression Diagnostics: Identifying Influential data and Sources of Collinearity. Wiley, New York (1980).
40. Cook R. D., Weisberg S.: Residuals and Influence in Regression. Chapman & Hall, London (1982).
41. Atkinson A. C.: Plots, Transformations and Regression: An Introduction to Graphical Methods of Diagnostic Regression Analysis. Claredon Press, Oxford (1985).
42. Chatterjee S., Hadi A. S.: Sensitivity Analysis in Linear Regression. Wiley, New York (1988).
43. Barnett V., Lewis T.: Outliers in Statistical Data. 2nd edn. Wiley, New York (1984).
44. R. E. Welsch, Linear Regression Diagnostics, Technical Report 923-77, Sloan School of Management, Massachusetts Institute of Technology, (1977).
45. Weisberg S.: Applied Linear Regression. Wiley, New York (1985).
46. Rousseeuw P. J., Leroy A. M.: Robust Regression and Outlier Detection. Wiley, New York (1987).