Literature DB >> 26290258

Tales from the war on error: the art and science of curating QSAR data.

Marvin Waldman1, Robert Fraczkiewicz1, Robert D Clark2.   

Abstract

Curating the data underlying quantitative structure-activity relationship models is a never-ending struggle. Some curation can now be automated but much cannot, especially where data as complex as those pertaining to molecular absorption, distribution, metabolism, excretion, and toxicity are concerned (vide infra). The authors discuss some particularly challenging problem areas in terms of specific examples involving experimental context, incompleteness of data, confusion of units, problematic nomenclature, tautomerism, and misapplication of automated structure recognition tools.

Entities:  

Keywords:  Automated structure recognition; Cytochrome P450; Data curation; Metabolism; Nomenclature; QSAR; Tautomerism

Mesh:

Substances:

Year:  2015        PMID: 26290258     DOI: 10.1007/s10822-015-9865-0

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  30 in total

1.  Utility of metabolic stability screening: comparison of in vitro and in vivo clearance.

Authors:  S E Clarke; P Jeffrey
Journal:  Xenobiotica       Date:  2001 Aug-Sep       Impact factor: 1.908

Review 2.  A literature review of enzyme kinetic parameters for CYP3A4-mediated metabolic reactions of 113 drugs in human liver microsomes: structure-kinetics relationship assessment.

Authors:  H-Z Bu
Journal:  Curr Drug Metab       Date:  2006-04       Impact factor: 3.731

3.  Discovery of potent and orally bioavailable heterocycle-based cannabinoid CB1 receptor agonists.

Authors:  Takao Kiyoi; Julia M Adam; John K Clark; Keneth Davies; Anna-Marie Easson; Darren Edwards; Helen Feilden; Ruth Fields; Stuart Francis; Fiona Jeremiah; Duncan McArthur; Angus J Morrison; Alan Prosser; Paul D Ratcliffe; Jurgen Schulz; Grant Wishart; James Baker; Robert Campbell; Jean E Cottney; Maureen Deehan; Ola Epemolu; Louise Evans
Journal:  Bioorg Med Chem Lett       Date:  2011-01-22       Impact factor: 2.823

Review 4.  N-glucuronidation of drugs and other xenobiotics by human and animal UDP-glucuronosyltransferases.

Authors:  Sanna Kaivosaari; Moshe Finel; Mikko Koskinen
Journal:  Xenobiotica       Date:  2011-03-24       Impact factor: 1.908

5.  Influence of phenylalanine-481 substitutions on the catalytic activity of cytochrome P450 2D6.

Authors:  G P Hayhurst; J Harlow; J Chowdry; E Gross; E Hilton; M S Lennard; G T Tucker; S W Ellis
Journal:  Biochem J       Date:  2001-04-15       Impact factor: 3.857

6.  Development of dual PLD1/2 and PLD2 selective inhibitors from a common 1,3,8-Triazaspiro[4.5]decane Core: discovery of Ml298 and Ml299 that decrease invasive migration in U87-MG glioblastoma cells.

Authors:  Matthew C O'Reilly; Sarah A Scott; Kyle A Brown; Thomas H Oguin; Paul G Thomas; J Scott Daniels; Ryan Morrison; H Alex Brown; Craig W Lindsley
Journal:  J Med Chem       Date:  2013-03-13       Impact factor: 7.446

7.  Quantitative structure-metabolism relationship modeling of metabolic N-dealkylation reaction rates.

Authors:  Konstantin V Balakin; Sean Ekins; Andrey Bugrim; Yan A Ivanenkov; Dmitry Korolev; Yuri V Nikolsky; Andrey A Ivashchenko; Nikolay P Savchuk; Tatiana Nikolskaya
Journal:  Drug Metab Dispos       Date:  2004-07-21       Impact factor: 3.922

Review 8.  The enol tautomer of indole-3-pyruvic acid as a biological switch in stress responses.

Authors:  Barbara Bartolini; Cristina Corniello; Antonio Sella; Francesca Somma; Vincenzo Politi
Journal:  Adv Exp Med Biol       Date:  2003       Impact factor: 2.622

9.  Using beta binomials to estimate classification uncertainty for ensemble models.

Authors:  Robert D Clark; Wenkel Liang; Adam C Lee; Michael S Lawless; Robert Fraczkiewicz; Marvin Waldman
Journal:  J Cheminform       Date:  2014-06-22       Impact factor: 5.514

10.  How accurately can we predict the melting points of drug-like compounds?

Authors:  Igor V Tetko; Yurii Sushko; Sergii Novotarskyi; Luc Patiny; Ivan Kondratov; Alexander E Petrenko; Larisa Charochkina; Abdullah M Asiri
Journal:  J Chem Inf Model       Date:  2014-12-09       Impact factor: 4.956

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  1 in total

Review 1.  Predicting mammalian metabolism and toxicity of pesticides in silico.

Authors:  Robert D Clark
Journal:  Pest Manag Sci       Date:  2018-05-15       Impact factor: 4.845

  1 in total

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