Erratum: 13C NMR-Distance matrix descriptors: Optimal abstract 3D space granularity for predicting estrogen binding (Journal of Chemical Information and Modeling (2012) 52: 7 (1854-1864) DOI: 10.1021/ci3001698);13C NMR-distance matrix descriptors: Optimal abstract 3D space granularity for predicting estrogen binding

Journal of Chemical Information and Modeling

Volumn 52, Issue 7, 2012, Pages 1854-1864

  Slavov, Svetoslav H ^a   Geesaman, Elizabeth L ^a   Pearce, Bruce A ^a   Schnackenberg, Laura K ^a   Buzatu, Dan A ^a   Wilkes, Jon G ^a   Beger, Richard D ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDERS; KNOWLEDGE BASED SYSTEMS; LEAST SQUARES APPROXIMATIONS;

DIFFERENT GRANULARITIES; DISTANCE MATRICES; ENDOCRINE DISRUPTOR; ESTIMATION ERRORS; ESTROGEN RECEPTOR; INTER-ATOMIC DISTANCES; PARTIAL LEAST SQUARE (PLS); STRUCTURAL FEATURE;

CHEMICAL SHIFT;

ESTROGEN; ESTROGEN RECEPTOR;

BINDING SITE; CHEMISTRY; FORECASTING; METABOLISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; QUANTITATIVE STRUCTURE ACTIVITY RELATION; ARTICLE;

BINDING SITES; ESTROGENS; FORECASTING; MAGNETIC RESONANCE SPECTROSCOPY; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTORS, ESTROGEN;

EID: 84864248786     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300389y     Document Type: Erratum

References (52)

1. Cramer, R. D. BC(DEF) Parameters. 1. The intrinsic dimensionality of intermolecular interactions in the liquid state J. Am. Chem. Soc. 1980, 102, 1837-1849
2. Abraham, M. H. Scales of solute hydrogen-bonding: Their construction and application to physicochemical and biochemical processes Chem. Soc. Rev. 1993, 22, 73-83
3. Labute, P. A widely applicable set of descriptors J. Mol. Graph. Model. 2000, 18, 464-477 (Pubitemid 32260549)
4. Cherkasov, A. Inductive QSAR descriptors. Distinguishing compounds with antibacterial activity by artificial neural networks Int. J. Mol. Sci. 2005, 6, 63-86 (Pubitemid 40318073)
5. Bersuker, I. QSAR without arbitrary descriptors: The electron- conformational method J. Comput. Aided Mol. Des. 2008, 22, 423-430
6. Burden, F. R.; Polley, M. J.; Winkler, D. A. Toward novel universal descriptors: Charge fingerprints J. Chem. Inf. Model. 2009, 49, 710-715
7. Andersson, P.; Haglund, P.; Rappe, C.; Tysklind, M. Ultraviolet absorption characteristics and calculated semi-empirical parameters as chemical descriptors in multivariate modelling of polychlorinated biphenyls J. Chemometrics 1996, 10, 171-185 (Pubitemid 126469182)
8. Benigni, R.; Giuliani, A.; Passerini, L. Infrared spectra as chemical descriptors for QSAR models J. Chem. Inf. Comput. Sci. 2001, 41, 727-730
9. 13C NMR chemical shift as QSAR/QSPR descriptor Chem. Rev. 2011, 111, 2865-2899
10. Levy, J. B. A quantum chemical and electrostatic study of alkyl and substituted benzenonium cations and related molecules: The effect of atomic charge distribution on carbocation energy and geometry Struct. Chem. 1999, 10, 121-127 (Pubitemid 129644386)
11. Lin, S.-T.; Lee, C.-C.; Liang, D. W. Analysis of substituent effects on C-13 NMR parameters of substituted arylacetylene derivatives. Linear free energy relationships and PM3 semiempirical calculations Tetrahedron 2000, 56, 9619-9623
12. 13C NMR chemical shifts, ν(CO) frequency values, charge densities, and isodesmic reactions to interprete substituent effects on reactivity J. Org. Chem. 2002, 67, 6995-7003
13. Thirunarayanan, G. IR and NMR spectral studies in substituted styryl 1-naphthyl ketones Acta Cienc. Indica 2005, 31, 299-304
14. Xu, R.; Sim, M. K.; Go, M. L. Synthesis, Antimuscarinic activity and quantitative structure-activity relationship (QSAR) of tropinyl and piperidinyl esters Chem. Pharm. Bull. 1998, 46, 231-241 (Pubitemid 28126401)
15. 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
16. 13C NMR and EI Mass spectrometric data-activity relationship model of estrogen receptor binding Toxicol. Appl. Pharmacol. 2000, 169, 17-25
17. 13C NMR spectrometric data to produce a predictive model of estrogen receptor binding activity J. Chem. Inf. Comput. Sci. 2001, 41, 219-224 (Pubitemid 33645692)
18. 13C NMR quantitative spectrometric data-activity relationship (QSDAR) models of steroid binding to the corticosteroid binding globulin J. Comput.-Aided Mol. Design. 2001, 15, 659-669 (Pubitemid 32962605)
19. 13C NMR quantitative spectrometric data-activity relationship (QSDAR) models of steroids binding the aromatase enzyme J. Chem. Inf. Comput. Sci. 2001, 41, 1360-1366
20. 13C NMR data J. Chem. Inf. Comput. Sci. 2001, 41, 1322-1329
21. Beger, R. D.; Buzatu, D. A.; Wilkes, J. G.; Lay, J. O., Jr. Comparative structural connectivity spectra analysis (CoSCoSA) models of steroid binding to the corticosteroid binding globulin J. Chem. Inf. Comput. Sci. 2002, 42, 1123-1131 (Pubitemid 35360295)
22. Beger, R. D.; Buzatu, D. A.; Wilkes, J. G. Combining NMR spectral and structural data to form models of polychlorinated dibenzodioxins, dibenzofurans, and biphenyls binding to the AhR J. Comput. Aided Mol. Des. 2002, 16, 727-740 (Pubitemid 36336182)
23. nd ed.; Shayne, C. G., Ed.; John Wiley & Sons: Hoboken, NJ, 2005; pp 227-286.
24. Thirunarayanan, G. IR and NMR spectral studies in substituted styryl 1-naphthyl ketones Acta Cienc. Indica,Chem. 2005, 31, 299-304
25. Beger, R. D. Computational modeling of biologically active molecules using NMR spectra Drug Discovery Today 2006, 11, 429-435
26. Ning, Y.-C. Interpretation of Organic Spectra; John Wiley and Sons (Asia) Pte Ltd: Singapore, 2011; p 41.
27. Wilman, D. E.V.; Palmer, B. D.; Denny, W. A. Application of 15N nuclear magnetic resonance spectroscopy to the determination of the stability of aryl nitrogen mustards J. Med. Chem. 1995, 38, 2256-2258
28. 15N chemical shift differences in MMP-3 ligands Bioorg. Med. Chem. Lett. 2005, 15, 1779-1783 (Pubitemid 40380731)
29. Shade, L.; Beger, R. D.; Wilkes, J. G. The use of carbon thirteen nuclear magnetic resonance spectra to predict dioxin and furan binding affinities to the aryl hydrocarbon receptor Environ. Toxicol. Chem. 2003, 22, 501-509 (Pubitemid 36231816)
30. Miller, D. W.; Beger, R.; Lay, J. O., Jr.; Wilkes, J. G.; Freeman, J. P. WO 2001057495 A2 20010809, 2001.
31. Miller, D. W.; Beger, R.; Lay, J. O., Jr.; Wilkes, J. G.; Freeman, J. P. US 6898533 B1 20050524, 2005.
32. Beger, R. D.; Wilkes, J. G. US 20030229456 A1 20031211, 2003.
33. Wang, Y.; Li, Y.; Ding, J.; Wang, Y.; Chang, Y. Prediction of binding affinity for estrogen receptor α modulators using statistical learning approaches Mol. Divers. 2008, 12, 93-102
34. Abdi, H. Partial least squares regression and projection on latent structure regression (PLS regression) WIREs Comp Stat. 2010, 2, 97-106
35. Swan, S. H.; Elkin, E. P.; Fenster, L. The question of declining sperm density revisited: An analysis of 101 studies published 1934-1996 Environ. Health Perspect. 2000, 108, 961-966
36. Joensen, U. N.; Jorgensen, N.; Rajpert-De Meyts, E.; Skakkebaek, N. E. Testicular dysgenesis syndrome and leydig cell function Basic Clin. Pharmacol. Toxicol. 2008, 102, 155-161 (Pubitemid 351143441)
37. Cleary, M. P.; Grossmann, M. E. Obesity and breast cancer: The estrogen connection Endocrinology 2009, 150, 2537-2542
38. Diamanti-Kandarakis, E.; Palioura, E.; Kandarakis, S. A.; Koutsilieris, M. The impact of endocrine disruptors on endocrine targets Horm. Metab. Res. 2010, 42, 543-552
39. Endocrine Disruptors Knowledge Base. http://www.fda.gov/ScienceResearch/ BioinformaticsTools/EndocrineDisruptorKnowledgebase/ucm136091.htm (accessed 02/14/ 2012).
40. Shi, L. M.; Fang, H.; Tong, W.; Wu, J.; Perkins, R.; Blair, R. M.; Branham, W. S.; Dial, S. L.; Moland, C. L.; Sheehan, D. M. QSAR models using a large diverse set of estrogens J. Chem. Inf. Comput. Sci. 2001, 41, 186-195 (Pubitemid 33645689)
41. Ghafourian, T.; Cronin, M. T. The impact of variable selection on the modelling of oestrogenicity SAR QSAR Environ. Res. 2005, 16, 171-190 (Pubitemid 40623248)
42. Marini, F.; Roncaglioni, A.; Nović, M. Variable selection and interpretation in structure-affinity correlation modeling of estrogen receptor binders J. Chem. Inf. Model. 2005, 45, 1507-1519 (Pubitemid 41784716)
43. Doweyko, A. M.; Bell, A. R.; Minatelli, J. A.; Relyea, D. I. Quantitative structure-activity relationships for 2-[(phenylmethyl)sulfonyl]pyridine 1-oxide herbicides J. Med. Chem. 1983, 26, 475-478 (Pubitemid 13162287)
44. HyperChem 8 Tools for Molecular Modeling, version 8.0; HyperCube Inc.: Gainesville, FL, 2007.
45. ACD/NMR Predictor Release 12.00, version 12.5; Advanced Chemistry Development: Toronto, Canada, 2011.
46. Bremser, W. HOSE: A novel substructure code Anal. Chim. Acta 1978, 103, 355-365
47. R Statistical Package [Online], version v.2.13.2. www.r-project.org (accessed 02/14/ 2012).
48. nd ed.; Kluwer: Boston, MA, 2003; p 413.
49. Beger, R. D.; Buzatu, D. A.; Wilkes, J. G. Quantitative spectrometric data-activity relationships (QSDAR) models of endocrine disruptor binding activities; CRC Press: Boca Raton, FL, 2009, pp 237-260.
50. 2! J. Mol. Graph. Model. 2002, 20, 269-276 (Pubitemid 34017544)
51. 17O NMR Spectroscopy in Organic Chemistry; CRC Press: Boca Raton, FL, 1991; pp 2-22.
52. Sugimura, T.; Wakabayashi, K.; Nakagama, H.; Nagao, M. Heterocyclic amines: Mutagens/carcinogens produced during cooking of meat and fish Cancer Sci. 2004, 95, 290-299 (Pubitemid 38519467)