QSAR as a random event: criteria of predictive potential for a chance model
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Abstract
The CORAL software (http://www.insilico.eu/coral) was suggested as a tool to build up quantitative structure–property/activity relationships (QSPRs/QSARs). This software is based on conception “a QSPR/QSAR model should be interpreted as a random event.” This is reflection of fact: different distributions into the training set (substances involved in modeling process) and the validation set (substances, which are not known at the moment of the modeling process) give models with significant dispersion in the statistical quality of the QSPR/QSAR. Results of experiments with the software and possible ways of further improvement of this software are discussed. The most attractive new ways to estimate predictive potential of the CORAL model seem to be the following ones: (i) index of ideality of correlation and (ii) correlation contradiction index. These can be also proposed as criteria of predictive potential for arbitrary QSPR/QSAR.
Keywords
QSPR/QSAR Monte Carlo method Random event Index of ideality of correlation Correlation contradiction index Validation CORAL softwareNotes
Acknowledgements
The authors express gratitude to the administration of Istituto di Ricerche Farmacologiche Mario Negri for possibility to carry out this research.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
References
- 1.Doweyko AM (2008). J Comput Aided Mol Des 22(2):81–89CrossRefPubMedGoogle Scholar
- 2.Johnson SR (2008). J Chem Inf Model 48(1):25–26CrossRefPubMedGoogle Scholar
- 3.Toropova AP, Toropov AA, Benfenati E, Leszczynska D, Leszczynski J (2015). Bioorg Med Chem 23(6):1223–1230CrossRefPubMedGoogle Scholar
- 4.Toropov AA, Toropova AP, Puzyn T, Benfenati E, Gini G, Leszczynska D, Leszczynski J (2013). Chemosphere 92(1):31–37CrossRefPubMedGoogle Scholar
- 5.Duchowicz PR, Bacelo DE, Fioressi SE, Palermo V, Ibezim NE, Romanelli GP (2018). Med Chem Res 27(2):420–428CrossRefGoogle Scholar
- 6.Fioressi SE, Bacelo DE, Rojas C, Aranda JF, Duchowicz PR (2019). Ecotoxicol Environ Saf 171:47–53CrossRefPubMedGoogle Scholar
- 7.Rücker C, Rücker G, Meringer M (2007). J Chem Inf Model 47(6):2345–2357CrossRefPubMedGoogle Scholar
- 8.Consonni V, Ballabio D, Todeschini R (2009). J Chem Inf Model 49(7):1669–1678CrossRefPubMedGoogle Scholar
- 9.Toropova AP, Toropov AA (2019). Mol Inf 38:1800157CrossRefGoogle Scholar
- 10.Golbraikh A, Shen M, Xiao Z, Xiao Y-D, Lee K-H, Tropsha A (2003). J Comput Aided Mol Des 17(2–4):241–253CrossRefPubMedGoogle Scholar
- 11.Gaikwad R, Ghorai S, Amin SA, Adhikari N, Patel T, Das K, Jha T, Gayen S (2018). Toxicol in Vitro 52:23–32CrossRefPubMedGoogle Scholar
- 12.Simon L, Imane A, Srinivasan KK, Pathak L, Daoud I (2017). Interdiscip Sci Comput Life Sci 9(3):445–458CrossRefGoogle Scholar
- 13.Ahmadi S, Mardinia F, Azimi N, Qomi M, Balali E (2019). J Mol Struct 1181:305–311CrossRefGoogle Scholar
- 14.Stoičkov V, Šarić S, Golubović M, Zlatanović D, Krtinić D, Dinić L, Mladenović B, Sokolović D, Veselinović AM (2018). SAR QSAR Environ Res 29(7):503–515CrossRefPubMedGoogle Scholar
- 15.Achary PGR (2014). SAR QSAR Environ Res 25(1):73–90CrossRefPubMedGoogle Scholar
- 16.Živković JV, Trutić NV, Veselinović JB, Nikolić GM, Veselinović AM (2015). Comput Biol Med 64:276–282CrossRefPubMedGoogle Scholar
- 17.Kumar P, Kumar A, Sindhu J (2019). SAR QSAR Environ Res 30(2):63–80CrossRefPubMedGoogle Scholar
- 18.Begum S, Achary PGR (2015). SAR QSAR Environ Res 26(5):343–361CrossRefPubMedGoogle Scholar
- 19.Kumar P, Kumar A (2018). Drug Res 68(4):189–195CrossRefGoogle Scholar
- 20.Ćirić Zdravković S, Pavlović M, Apostlović S, Koraćević G, Šalinger Martinović S, Stanojević D, Sokolović D, Veselinović AM (2019). Comput Biol Chem 79:55–62CrossRefPubMedGoogle Scholar
- 21.Trinh TX, Choi J-S, Jeon H, Byun H-G, Yoon T-H, Kim J (2018). Chem Res Toxicol 31(3):183–190CrossRefPubMedGoogle Scholar
- 22.Heidari A, Fatemi MH (2017). J Chin Chem Soc 64(3):289–295CrossRefGoogle Scholar
- 23.Ahmadi S, Akbari A (2018). SAR QSAR Environ Res 29(11):895–909CrossRefPubMedGoogle Scholar
- 24.Bhargava S, Adhikari N, Amin SA, Das K, Gayen S, Jha T (2017). SAR QSAR Environ Res 28(12):973–990CrossRefPubMedGoogle Scholar
- 25.Islam MA, Pillay TS (2016). Chemom Intell Lab Syst 153:67–74CrossRefGoogle Scholar
- 26.Halder AK (2018). SAR QSAR Environ Res 29(11):911–933CrossRefPubMedGoogle Scholar
- 27.Golubović M, Lazarević M, Zlatanović D, Krtinić D, Stoičkov V, Mladenović B, Milić DJ, Sokolović D, Veselinović AM (2018). Comput Biol Chem 75:32–38CrossRefPubMedGoogle Scholar
- 28.Stoičkov V, Stojanović D, Tasić I, Šarić S, Radenković D, Babović P, Sokolović D, Veselinović AM (2018). Struct Chem 29(2):441–449CrossRefGoogle Scholar
- 29.Veselinović JB, Đorđević V, Bogdanović M, Morić I, Veselinović AM (2018). Struct Chem 29(2):541–551CrossRefGoogle Scholar
- 30.Amin SA, Bhargava S, Adhikari N, Gayen S, Jha T (2018). J Biomol Struct Dyn 36(3):590–608CrossRefPubMedGoogle Scholar
- 31.Zdravković M, Antović A, Veselinović JB, Sokolović D, Veselinović AM (2018). Talanta 178:656–662CrossRefPubMedGoogle Scholar
- 32.Kumar A, Chauhan S (2017). SAR QSAR Environ Res 28(3):179–197CrossRefPubMedGoogle Scholar
- 33.Kumar A, Chauhan S (2018). Future Med Chem 10(13):1603–1622CrossRefPubMedGoogle Scholar
- 34.Amata E, Marrazzo A, Dichiara M, Modica MN, Salerno L, Prezzavento O, Nastasi G, Rescifina A, Romeo G, Pittalà V (2017). ChemMedChem 12(22):1873–1881CrossRefPubMedGoogle Scholar
- 35.Rescifina A, Floresta G, Marrazzo A, Parenti C, Prezzavento O, Nastasi G, Dichiara M, Amata E (2017). Eur J Pharm Sci 106:94–101CrossRefPubMedGoogle Scholar
- 36.Sokolović D, Ranković J, Stanković V, Stefanović R, Karaleić S, Mekić B, Milenković V, Kocić J, Veselinović AM (2017). Med Chem Res 26(4):796–804CrossRefGoogle Scholar
- 37.Kumar A, Chauhan S (2017). Arch Pharm 350(1):e1600268CrossRefGoogle Scholar
- 38.Kumar A, Chauhan S (2017). Drug Res 67(3):156–162Google Scholar
- 39.Sokolović D, Aleksić D, Milenković V, Karaleić S, Mitić D, Kocić J, Mekić B, Veselinović JB, Veselinović AM (2016). Med Chem Res 25(12):2989–2998CrossRefGoogle Scholar
- 40.Sokolović D, Stanković V, Toskić D, Lilić L, Ranković G, Ranković J, Nedin-Ranković G, Veselinović AM (2016). Struct Chem 27(5):1511–1519CrossRefGoogle Scholar
- 41.Toropova MA (2017). Curr Drug Metab 18(12):1123–1131CrossRefPubMedGoogle Scholar
- 42.Mondal C, Halder AK, Adhikari N, Saha A, Saha KD, Gayen S, Jha T (2015). Eur J Med Chem 90:860–875CrossRefPubMedGoogle Scholar
- 43.Veselinović JB, Nikolić GM, Trutić NV, Živković JV, Veselinović AM (2015). SAR QSAR Environ Res 26(6):449–460CrossRefPubMedGoogle Scholar
- 44.Li Q, Ding X, Si H, Gao H (2014). Chemom Intell Lab Syst 139:132–138CrossRefGoogle Scholar
- 45.Achary PGR (2014). SAR QSAR Environ Res 25(6):507–526CrossRefPubMedGoogle Scholar
- 46.Garro Martinez JC, Duchowicz PR, Estrada MR, Zamarbide GN, Castro EA (2011). Int J Mol Sci 12(12):9354–9368CrossRefPubMedPubMedCentralGoogle Scholar
- 47.Toropov AA, Toropova AP (2019). Toxicol Mech Methods 29:43–52CrossRefPubMedGoogle Scholar
- 48.Ojha PK, Mitra I, Das RN, Roy K (2011). Chemom Intell Lab Syst 107(1):194–205CrossRefGoogle Scholar
- 49.I-Kuei Lin L (1989). Biometrics 45(1):255–268CrossRefPubMedGoogle Scholar
- 50.Toropov AA, Toropova AP (2017). Mutat Res Genet Toxicol Environ Mutagen 819:31–37CrossRefGoogle Scholar
- 51.Toropov AA, Carbó-Dorca R, Toropova AP (2018). Struct Chem 29(1):33–38CrossRefGoogle Scholar
- 52.Toropova AP, Toropov AA (2019). J Mol Struct 1182:141–149CrossRefGoogle Scholar
- 53.Toropov AA, Raška I, Toropova AP, Raškova M, Veselinović AM, Veselinović JB (2019). Sci Total Environ 659:1387–1394CrossRefPubMedGoogle Scholar
- 54.Toropova AP, Toropov AA, Veselinović AM, Veselinović JB, Leszczynska D, Leszczynski J (2019). Mol Cell Biochem 452(1–2):133–140CrossRefPubMedGoogle Scholar
- 55.Basak SC, Mills DR, Balaban AT, Gute BD (2001). J Chem Inf Comput Sci 41(3):671–678CrossRefPubMedGoogle Scholar