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Volumn 56, Issue 7, 2016, Pages 1243-1252

Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

EID: 84979530276     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.6b00129     Document Type: Review
Times cited : (224)

References (54)
  • 2
    • 84979612884 scopus 로고    scopus 로고
    • ChEMBL Database. (accessed March 1)
    • ChEMBL Database. https://www.ebi.ac.uk/chembl/ (accessed March 1, 2016).
    • (2016)
  • 3
    • 84979504731 scopus 로고    scopus 로고
    • PubChem. (accessed March 1)
    • PubChem. http://pubchem.ncbi.nlm.nih.gov/ (accessed March 1, 2016).
    • (2016)
  • 4
    • 84979609636 scopus 로고    scopus 로고
    • PDSP. (accessed March 1)
    • PDSP. http://pdsp.med.unc.edu (accessed March 1, 2016).
    • (2016)
  • 5
    • 84899415084 scopus 로고    scopus 로고
    • Learning from "big Data": Compounds and Targets
    • Hu, Y.; Bajorath, J. Learning from "Big Data": Compounds and Targets Drug Discovery Today 2014, 19, 357-360 10.1016/j.drudis.2014.02.004
    • (2014) Drug Discovery Today , vol.19 , pp. 357-360
    • Hu, Y.1    Bajorath, J.2
  • 11
    • 58149136373 scopus 로고    scopus 로고
    • Are the Chemical Structures in Your QSAR Correct?
    • Young, D.; Martin, D.; Venkatapathy, R.; Harten, P. Are the Chemical Structures in Your QSAR Correct? QSAR Comb. Sci. 2008, 27, 1337-1345 10.1002/qsar.200810084
    • (2008) QSAR Comb. Sci. , vol.27 , pp. 1337-1345
    • Young, D.1    Martin, D.2    Venkatapathy, R.3    Harten, P.4
  • 12
    • 80055088241 scopus 로고    scopus 로고
    • Believe It or Not: How Much Can We Rely on Published Data on Potential Drug Targets?
    • Prinz, F.; Schlange, T.; Asadullah, K. Believe It or Not: How Much Can We Rely on Published Data on Potential Drug Targets? Nat. Rev. Drug Discovery 2011, 10, 712 10.1038/nrd3439-c1
    • (2011) Nat. Rev. Drug Discovery , vol.10 , pp. 712
    • Prinz, F.1    Schlange, T.2    Asadullah, K.3
  • 13
    • 84859169880 scopus 로고    scopus 로고
    • Drug Development: Raise Standards for Preclinical Cancer Research
    • Begley, C. G.; Ellis, L. M. Drug Development: Raise Standards for Preclinical Cancer Research Nature 2012, 483, 531-533 10.1038/483531a
    • (2012) Nature , vol.483 , pp. 531-533
    • Begley, C.G.1    Ellis, L.M.2
  • 14
    • 84862276184 scopus 로고    scopus 로고
    • The Experimental Uncertainty of Heterogeneous Public K(i) Data
    • Kramer, C.; Kalliokoski, T.; Gedeck, P.; Vulpetti, A. The Experimental Uncertainty of Heterogeneous Public K(i) Data J. Med. Chem. 2012, 55, 5165-5173 10.1021/jm300131x
    • (2012) J. Med. Chem. , vol.55 , pp. 5165-5173
    • Kramer, C.1    Kalliokoski, T.2    Gedeck, P.3    Vulpetti, A.4
  • 15
    • 84877067898 scopus 로고    scopus 로고
    • Dispensing Processes Impact Apparent Biological Activity as Determined by Computational and Statistical Analyses
    • Ekins, S.; Olechno, J.; Williams, A. J. Dispensing Processes Impact Apparent Biological Activity as Determined by Computational and Statistical Analyses PLoS One 2013, 8, e62325 10.1371/journal.pone.0062325
    • (2013) PLoS One , vol.8 , pp. e62325
    • Ekins, S.1    Olechno, J.2    Williams, A.J.3
  • 16
    • 85029156735 scopus 로고    scopus 로고
    • Facilitating Reproducibility
    • Editorial
    • Editorial. Facilitating Reproducibility Nat. Chem. Biol. 2013, 9, 345 10.1038/nchembio.1269
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 345
  • 17
    • 84893351797 scopus 로고    scopus 로고
    • Policy: NIH Plans to Enhance Reproducibility
    • Collins, F. S.; Tabak, L. A. Policy: NIH Plans to Enhance Reproducibility Nature 2014, 505, 612-613 10.1038/505612a
    • (2014) Nature , vol.505 , pp. 612-613
    • Collins, F.S.1    Tabak, L.A.2
  • 18
    • 84955453295 scopus 로고    scopus 로고
    • Repetitive Flaws
    • Editorial
    • Editorial. Repetitive Flaws Nature 2016, 529, 256 10.1038/529256a
    • (2016) Nature , vol.529 , pp. 256
  • 19
    • 84961363486 scopus 로고    scopus 로고
    • Joining the Reproducibility Initiative
    • Editorial
    • Editorial. Joining the Reproducibility Initiative Nat. Nanotechnol. 2014, 9, 949 10.1038/nnano.2014.287
    • (2014) Nat. Nanotechnol. , vol.9 , pp. 949
  • 20
    • 84979631089 scopus 로고    scopus 로고
    • National Institute of Health. NIH Rigor and Reproducibility. (accessed May 25)
    • National Institute of Health. NIH Rigor and Reproducibility. https://www.nih.gov/research-training/rigor-reproducibility (accessed May 25, 2016).
    • (2016)
  • 21
    • 78049349961 scopus 로고    scopus 로고
    • Trust, but Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research
    • Fourches, D.; Muratov, E.; Tropsha, A. Trust, but Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research J. Chem. Inf. Model. 2010, 50, 1189-1204 10.1021/ci100176x
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1189-1204
    • Fourches, D.1    Muratov, E.2    Tropsha, A.3
  • 23
    • 76249106208 scopus 로고    scopus 로고
    • Let's Not Forget Tautomers
    • Martin, Y. C. Let's Not Forget Tautomers J. Comput.-Aided Mol. Des. 2009, 23, 693-704 10.1007/s10822-009-9303-2
    • (2009) J. Comput.-Aided Mol. Des. , vol.23 , pp. 693-704
    • Martin, Y.C.1
  • 25
    • 84979626928 scopus 로고    scopus 로고
    • ChemAxon. (accessed March 1)
    • ChemAxon. http://www.chemaxon.com (accessed March 1, 2016).
    • (2016)
  • 26
    • 84979532102 scopus 로고    scopus 로고
    • RDKit. (accessed March 1)
    • RDKit. http://www.rdkit.org/ (accessed March 1, 2016).
    • (2016)
  • 27
    • 84979532100 scopus 로고    scopus 로고
    • Schrodinger. LigPrep. (accessed Mar 1)
    • Schrodinger. LigPrep. http://www.schrodinger.com/LigPrep/ (accessed Mar 1, 2016).
    • (2016)
  • 28
    • 84979552368 scopus 로고    scopus 로고
    • KNIME. (accessed March 1)
    • KNIME. http://www.knime.org/ (accessed March 1, 2016).
    • (2016)
  • 30
    • 84979525116 scopus 로고    scopus 로고
    • ChemSpider. (accessed March 1)
    • ChemSpider. http://www.chemspider.com (accessed March 1, 2016).
    • (2016)
  • 34
    • 44249116058 scopus 로고    scopus 로고
    • Hierarchical QSAR Technology Based on the Simplex Representation of Molecular Structure
    • Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N. Hierarchical QSAR Technology Based on the Simplex Representation of Molecular Structure J. Comput.-Aided Mol. Des. 2008, 22, 403-421 10.1007/s10822-008-9179-6
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 403-421
    • Kuz'Min, V.E.1    Artemenko, A.G.2    Muratov, E.N.3
  • 35
    • 84876174816 scopus 로고    scopus 로고
    • Comparability of Mixed IC50 Data - A Statistical Analysis
    • Kalliokoski, T.; Kramer, C.; Vulpetti, A.; Gedeck, P. Comparability of Mixed IC50 Data-a Statistical Analysis PLoS One 2013, 8, e61007 10.1371/journal.pone.0061007
    • (2013) PLoS One , vol.8 , pp. e61007
    • Kalliokoski, T.1    Kramer, C.2    Vulpetti, A.3    Gedeck, P.4
  • 36
    • 84894581873 scopus 로고    scopus 로고
    • HTS Navigator: Freely-Accessible Cheminformatics Software for Analyzing High-Throughput Screening Data
    • Fourches, D.; Sassano, M. F.; Roth, B. L.; Tropsha, A. HTS Navigator: Freely-Accessible Cheminformatics Software for Analyzing High-Throughput Screening Data Bioinformatics 2014, 30, 588-589 10.1093/bioinformatics/btt718
    • (2014) Bioinformatics , vol.30 , pp. 588-589
    • Fourches, D.1    Sassano, M.F.2    Roth, B.L.3    Tropsha, A.4
  • 37
    • 0023677902 scopus 로고
    • Computer-Assisted Analysis of Interlaboratory Ames Test Variability
    • Benigni, R.; Giuliani, A. Computer-Assisted Analysis of Interlaboratory Ames Test Variability J. Toxicol. Environ. Health 1988, 25, 135-148 10.1080/15287398809531194
    • (1988) J. Toxicol. Environ. Health , vol.25 , pp. 135-148
    • Benigni, R.1    Giuliani, A.2
  • 39
    • 16544372352 scopus 로고    scopus 로고
    • Randomized Phase III Trial of Marimastat versus Placebo in Patients with Metastatic Breast Cancer Who Have Responding or Stable Disease after First-Line Chemotherapy: Eastern Cooperative Oncology Group Trial E2196
    • Sparano, J. A.; Bernardo, P.; Stephenson, P.; Gradishar, W. J.; Ingle, J. N.; Zucker, S.; Davidson, N. E. Randomized Phase III Trial of Marimastat versus Placebo in Patients with Metastatic Breast Cancer Who Have Responding or Stable Disease after First-Line Chemotherapy: Eastern Cooperative Oncology Group Trial E2196 J. Clin. Oncol. 2004, 22, 4683-4690 10.1200/JCO.2004.08.054
    • (2004) J. Clin. Oncol. , vol.22 , pp. 4683-4690
    • Sparano, J.A.1    Bernardo, P.2    Stephenson, P.3    Gradishar, W.J.4    Ingle, J.N.5    Zucker, S.6    Davidson, N.E.7
  • 40
    • 33746931581 scopus 로고    scopus 로고
    • On Outliers and Activity Cliffs - Why QSAR Often Disappoints
    • Maggiora, G. M. On Outliers and Activity Cliffs - Why QSAR Often Disappoints J. Chem. Inf. Model. 2006, 46, 1535 10.1021/ci060117s
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1535
    • Maggiora, G.M.1
  • 42
    • 84859169320 scopus 로고    scopus 로고
    • Exploration of 3D Activity Cliffs on the Basis of Compound Binding Modes and Comparison of 2D and 3D Cliffs
    • Hu, Y.; Bajorath, J. Exploration of 3D Activity Cliffs on the Basis of Compound Binding Modes and Comparison of 2D and 3D Cliffs J. Chem. Inf. Model. 2012, 52, 670-677 10.1021/ci300033e
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 670-677
    • Hu, Y.1    Bajorath, J.2
  • 43
    • 84883217252 scopus 로고    scopus 로고
    • Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches
    • Fourches, D.; Muratov, E.; Ding, F.; Dokholyan, N. V.; Tropsha, A. Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches J. Chem. Inf. Model. 2013, 53, 1915-1922 10.1021/ci400216q
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 1915-1922
    • Fourches, D.1    Muratov, E.2    Ding, F.3    Dokholyan, N.V.4    Tropsha, A.5
  • 46
    • 84955463767 scopus 로고    scopus 로고
    • Kernel Target Alignment Parameter: A New Modelability Measure for Regression Tasks
    • Marcou, G.; Horvath, D.; Varnek, A. Kernel Target Alignment Parameter: A New Modelability Measure for Regression Tasks J. Chem. Inf. Model. 2016, 56, 6-11 10.1021/acs.jcim.5b00539
    • (2016) J. Chem. Inf. Model. , vol.56 , pp. 6-11
    • Marcou, G.1    Horvath, D.2    Varnek, A.3
  • 47
    • 77956964002 scopus 로고    scopus 로고
    • Best Practices for QSAR Model Development, Validation, and Exploitation
    • Tropsha, A. Best Practices for QSAR Model Development, Validation, and Exploitation Mol. Inf. 2010, 29, 476-488 10.1002/minf.201000061
    • (2010) Mol. Inf. , vol.29 , pp. 476-488
    • Tropsha, A.1
  • 48
    • 84929366158 scopus 로고    scopus 로고
    • Predicting Chemically-Induced Skin Reactions. Part I: QSAR Models of Skin Sensitization and Their Application to Identify Potentially Hazardous Compounds
    • Alves, V. M.; Muratov, E.; Fourches, D.; Strickland, J.; Kleinstreuer, N.; Andrade, C. H.; Tropsha, A. Predicting Chemically-Induced Skin Reactions. Part I: QSAR Models of Skin Sensitization and Their Application to Identify Potentially Hazardous Compounds Toxicol. Appl. Pharmacol. 2015, 284, 262-272 10.1016/j.taap.2014.12.014
    • (2015) Toxicol. Appl. Pharmacol. , vol.284 , pp. 262-272
    • Alves, V.M.1    Muratov, E.2    Fourches, D.3    Strickland, J.4    Kleinstreuer, N.5    Andrade, C.H.6    Tropsha, A.7
  • 50
    • 84881185263 scopus 로고    scopus 로고
    • Pharmacokinetic-Pharmacodynamic Modeling of Antibacterial Drugs
    • Nielsen, E. I.; Friberg, L. E. Pharmacokinetic-Pharmacodynamic Modeling of Antibacterial Drugs Pharmacol. Rev. 2013, 65, 1053-1090 10.1124/pr.111.005769
    • (2013) Pharmacol. Rev. , vol.65 , pp. 1053-1090
    • Nielsen, E.I.1    Friberg, L.E.2
  • 53
    • 84923781144 scopus 로고    scopus 로고
    • Journals Unite for Reproducibility
    • Editorial
    • Editorial. Journals Unite for Reproducibility Nature 2014, 515, 7-8 10.1038/515007a
    • (2014) Nature , vol.515 , pp. 7-8
  • 54
    • 84959526076 scopus 로고    scopus 로고
    • Computer-Aided Design of Carbon Nanotubes with the Desired Bioactivity and Safety Profiles
    • Fourches, D.; Pu, D.; Li, L.; Zhou, H.; Mu, Q.; Su, G.; Yan, B.; Tropsha, A. Computer-Aided Design of Carbon Nanotubes with the Desired Bioactivity and Safety Profiles Nanotoxicology 2016, 10, 374-383 10.3109/17435390.2015.1073397
    • (2016) Nanotoxicology , vol.10 , pp. 374-383
    • Fourches, D.1    Pu, D.2    Li, L.3    Zhou, H.4    Mu, Q.5    Su, G.6    Yan, B.7    Tropsha, A.8


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