457
13 Continuous Molecular Fields Approach Applied to Structure-Activity Modeling
23. Kroemer RT, Hecht P (1995) Replacement of steric 6-12 potential–derived interaction energies by atom-based indicator variables in CoMFA leads to models of higher consistency. J
Comput-Aided Mol Des 9(3):205–212
24. Klebe G, Abraham U (1999) Comparative molecular similarity index analysis (CoMSIA)
to study hydrogen-bonding properties and to score combinatorial libraries. J Comput-Aided
Mol Des 13(1):1–10
25. Goodford P (2006) The basic principles of GRID. In: Cruciani G (ed) Molecular interaction
fields. Applications in drug discovery and ADME prediction. Methods and principles in medicinal chemistry, vol 27. Wiley-VCH, Weinheim, pp 3–26
26. Höskuldsson A (1988) PLS regression methods. J Chemom 2(3):211–228
27. Fradera X, Amat L, Besalu E, Carbo-Dorca R (1997) Application of molecular quantum
similarity to QSAR. Quant Struct-Act Rel 16(1):25–32
28. Rosipal R, Trejo LJ (2002) Kernel partial least squares regression in reproducing Kernel
Hilbert Space. J Mach Learn Res 2(2):97–123. doi:10.1162/15324430260185556
29. Baskin II, Tikhonova IG, Palyulin VA, Zefirov NS (2003) Selectivity fields: comparative
molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors. J Med Chem
46(19):4063–4069
30. Ramsay JO, Silverman BW (2005) Functional data analysis. Springer series in statistics, 2nd
edn. Springer, New York
31. Baskin II, Kireeva N, Varnek A (2010) The One-class classification approach to data description and to models applicability domain. Mol Inf 29(8–9):581–587. doi:10.1002/
minf.201000063
32. DePriest SA, Mayer D, Naylor CB, Marshall GR (1993) 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: a comparison of CoMFA models based on deduced
and experimentally determined active site geometries. J Am Chem Soc 115(13):5372–5384.
doi:10.1021/ja00066a004
33. Sutherland JJ, O’Brien LA, Weaver DF (2004) A comparison of methods for modeling quantitative structure-activity relationships. J Med Chem 47(22):5541–5554
34. Gohlke H, Klebe G (2002) DrugScore meets CoMFA: adaptation of fields for molecular
comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. J Med Chem 45(19):4153–4170. doi:10.1021/jm020808p
35. Böhm M, StüÑrzebecher J, Klebe G (1999) Three-Dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to
trypsin, thrombin, and factor Xa. J Med Chem 42(3):458–477. doi:10.1021/jm981062r
36. Besler BH, Merz KM, Kollman PA (1990) Atomic charges derived from semiempirical methods. J Comp Chem 11(4):431–439. doi:10.1002/jcc.540110404
37. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity-a rapid
access to atomic charges. Tetrahedron 36(22):3219–3228
38. Jaworska J, Nikolova-Jeliazkova N, Aldenberg T (2005) QSAR applicability domain estimation by projection of the training set in descriptor space: a review. Altern Lab Anim
33(5):445–459
39. Tetko IV, Sushko I, Pandey AK, Zhu H, Tropsha A, Papa E, Oberg T, Todeschini R, Fourches
D, Varnek A (2008) Critical assessment of QSAR models of environmental toxicity against
tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection. J Chem Inf Model 48(9):1733–1746. doi:10.1021/ci800151m
40. Sushko I, Novotarskyi S, Korner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen
K, Schroeter T, Muller KR, Xi L, Liu H, Yao X, Oberg T, Hormozdiari F, Dao P, Sahinalp
C, Todeschini R, Polishchuk P, Artemenko A, Kuz’min V, Martin TM, Young DM, Fourches
D, Muratov E, Tropsha A, Baskin I, Horvath D, Marcou G, Muller C, Varnek A, Prokopenko VV, Tetko IV (2010) Applicability domains for classification problems: Benchmarking of distance to models for Ames mutagenicity set. J Chem Inf Model 50(12):2094–2111.
doi:10.1021/ci100253r
13 Continuous Molecular Fields Approach Applied to Structure-Activity Modeling
23. Kroemer RT, Hecht P (1995) Replacement of steric 6-12 potential–derived interaction energies by atom-based indicator variables in CoMFA leads to models of higher consistency. J
Comput-Aided Mol Des 9(3):205–212
24. Klebe G, Abraham U (1999) Comparative molecular similarity index analysis (CoMSIA)
to study hydrogen-bonding properties and to score combinatorial libraries. J Comput-Aided
Mol Des 13(1):1–10
25. Goodford P (2006) The basic principles of GRID. In: Cruciani G (ed) Molecular interaction
fields. Applications in drug discovery and ADME prediction. Methods and principles in medicinal chemistry, vol 27. Wiley-VCH, Weinheim, pp 3–26
26. Höskuldsson A (1988) PLS regression methods. J Chemom 2(3):211–228
27. Fradera X, Amat L, Besalu E, Carbo-Dorca R (1997) Application of molecular quantum
similarity to QSAR. Quant Struct-Act Rel 16(1):25–32
28. Rosipal R, Trejo LJ (2002) Kernel partial least squares regression in reproducing Kernel
Hilbert Space. J Mach Learn Res 2(2):97–123. doi:10.1162/15324430260185556
29. Baskin II, Tikhonova IG, Palyulin VA, Zefirov NS (2003) Selectivity fields: comparative
molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors. J Med Chem
46(19):4063–4069
30. Ramsay JO, Silverman BW (2005) Functional data analysis. Springer series in statistics, 2nd
edn. Springer, New York
31. Baskin II, Kireeva N, Varnek A (2010) The One-class classification approach to data description and to models applicability domain. Mol Inf 29(8–9):581–587. doi:10.1002/
minf.201000063
32. DePriest SA, Mayer D, Naylor CB, Marshall GR (1993) 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: a comparison of CoMFA models based on deduced
and experimentally determined active site geometries. J Am Chem Soc 115(13):5372–5384.
doi:10.1021/ja00066a004
33. Sutherland JJ, O’Brien LA, Weaver DF (2004) A comparison of methods for modeling quantitative structure-activity relationships. J Med Chem 47(22):5541–5554
34. Gohlke H, Klebe G (2002) DrugScore meets CoMFA: adaptation of fields for molecular
comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. J Med Chem 45(19):4153–4170. doi:10.1021/jm020808p
35. Böhm M, StüÑrzebecher J, Klebe G (1999) Three-Dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to
trypsin, thrombin, and factor Xa. J Med Chem 42(3):458–477. doi:10.1021/jm981062r
36. Besler BH, Merz KM, Kollman PA (1990) Atomic charges derived from semiempirical methods. J Comp Chem 11(4):431–439. doi:10.1002/jcc.540110404
37. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity-a rapid
access to atomic charges. Tetrahedron 36(22):3219–3228
38. Jaworska J, Nikolova-Jeliazkova N, Aldenberg T (2005) QSAR applicability domain estimation by projection of the training set in descriptor space: a review. Altern Lab Anim
33(5):445–459
39. Tetko IV, Sushko I, Pandey AK, Zhu H, Tropsha A, Papa E, Oberg T, Todeschini R, Fourches
D, Varnek A (2008) Critical assessment of QSAR models of environmental toxicity against
tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection. J Chem Inf Model 48(9):1733–1746. doi:10.1021/ci800151m
40. Sushko I, Novotarskyi S, Korner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen
K, Schroeter T, Muller KR, Xi L, Liu H, Yao X, Oberg T, Hormozdiari F, Dao P, Sahinalp
C, Todeschini R, Polishchuk P, Artemenko A, Kuz’min V, Martin TM, Young DM, Fourches
D, Muratov E, Tropsha A, Baskin I, Horvath D, Marcou G, Muller C, Varnek A, Prokopenko VV, Tetko IV (2010) Applicability domains for classification problems: Benchmarking of distance to models for Ames mutagenicity set. J Chem Inf Model 50(12):2094–2111.
doi:10.1021/ci100253r