Computational Systems Biology Methods and Protocols.7z

(nextflipdebug5) #1

  1. ACD/Labs ToxSuite. Advanced Chemistry
    Development Inc., Toronto, Canada. Soft-
    ware available atwww.acdlabs.com

  2. Martin T Toxicity Estimation Software Tool
    (TEST). Software available atwww.epa.gov/
    nrmrl/std/qsar/qsar.html

  3. TOxicity Prediction by Komputer Assisted
    Technology (TOPKAT). Accelrys Inc., San
    Diego, USA. Software available athttp://
    accelrys.com

  4. ADMET Predictor. Simulations Plus Inc.,
    Lancaster, USA. Software available atwww.
    simulationsplus.com

  5. TerraQSAR. TerraBase Inc., Hamilton,
    Canada. Software available atwww.terrabase-
    inc.com

  6. Gonella Diaza R, Manganelli S, Esposito A,
    Roncaglioni A, Manganaro A, Benfenati E
    (2015) Comparison of in silico tools for eval-
    uating rat oral acute toxicity. SAR QSAR
    Environ Res 26(1):1–27.https://doi.org/
    10.1080/1062936x.2014.977819

  7. Drwal MN, Banerjee P, Dunkel M, Wettig
    MR, Preissner R (2014) ProTox: a web server
    for the in silico prediction of rodent oral tox-
    icity. Nucleic Acids Res 42(Web Server issue):
    W53–W58. https://doi.org/10.1093/nar/
    gku401.nar/gku401

  8. Muller L, Kikuchi Y, Probst G, Schechtman L,
    Shimada H, Sofuni T, Tweats D (1999)
    ICH-harmonised guidances on genotoxicity
    testing of pharmaceuticals: evolution,
    reasoning and impact. Mutat Res 436
    (3):195–225. https://doi.org/10.1016/
    s1383-5742(99)00004-6

  9. Lagunin AA, Dearden JC, Filimonov DA,
    Poroikov VV (2005) Computer-aided rodent
    carcinogenicity prediction. Mutat Res 586
    (2):138–146. https://doi.org/10.1016/j.
    mrgentox.2005.06.005

  10. Benigni R (2005) Structure-activity relation-
    ship studies of chemical mutagens and carci-
    nogens: mechanistic investigations and
    prediction approaches. Chem Rev 105
    (5):1767–1800. https://doi.org/10.1021/
    cr030049y

  11. Sato S, Tomita I (2001) Short-term screening
    method for the prediction of carcinogenicity
    of chemical substances: current status and
    problem of an in vivo rodent micronucleus
    assay. J Health Sci 47(1):1–8.https://doi.
    org/10.1248/jhs.47.1

  12. Benfenati E, Benigni R, Demarini DM,
    Helma C, Kirkland D, Martin TM,
    Mazzatorta P, Ouedraogo-Arras G, Richard
    AM, Schilter B, Schoonen WG, Snyder RD,
    Yang C (2009) Predictive models for


carcinogenicity and mutagenicity: frame-
works, state-of-the-art, and perspectives. J
Environ Sci Health C Environ Carcinog Eco-
toxicol Rev 27(2):57–90. https://doi.org/
10.1080/10590500902885593


  1. Kruhlak NL, Contrera JF, Benz RD, Mat-
    thews EJ (2007) Progress in QSAR toxicity
    screening of pharmaceutical impurities and
    other FDA regulated products. Adv Drug
    Deliv Rev 59(1):43–55.https://doi.org/10.
    1016/j.addr.2006.10.008

  2. Ashby J (1985) Fundamental structural alerts
    to potential carcinogenicity or noncarcino-
    genicity. Environ Mutagen 7(6):919–921.
    https://doi.org/10.1002/em.2860070613

  3. Bailey AB, Chanderbhan R, Collazo-Braier N,
    Cheeseman MA, Twaroski ML (2005) The
    use of structure-activity relationship analysis
    in the food contact notification program.
    Regul Toxicol Pharmacol 42(2):225–235.
    https://doi.org/10.1016/j.yrtph.2005.04.
    006

  4. Munro IC, Ford RA, Kennepohl E, Sprenger
    JG (1996) Thresholds of toxicological con-
    cern based on structure-activity relationships.
    Drug Metab Rev 28(1–2):209–217.https://
    doi.org/10.3109/03602539608994000

  5. Kazius J, McGuire R, Bursi R (2005) Deriva-
    tion and validation of toxicophores for muta-
    genicity prediction. J Med Chem 48
    (1):312–320. https://doi.org/10.1021/
    jm040835a

  6. Kazius J, Nijssen S, Kok J, Back T, Ijzerman
    AP (2006) Substructure mining using elabo-
    rate chemical representation. J Chem Inf
    Model 46(2):597–605.https://doi.org/10.
    1021/ci0503715

  7. Benigni R, Bossa C (2008) Structure alerts for
    carcinogenicity, and the Salmonella assay sys-
    tem: a novel insight through the chemical
    relational databases technology. Mutat Res
    659(3):248–261.https://doi.org/10.1016/
    j.mrrev.2008.05.003

  8. Wang Y, Lu J, Wang F, Shen Q, Zheng M,
    Luo X, Zhu W, Jiang H, Chen K (2012)
    Estimation of carcinogenicity using molecular
    fragments tree. J Chem Inf Model 52
    (8):1994–2003. https://doi.org/10.1021/
    ci300266p

  9. Kalgutkar AS, Didiuk MT (2009) Structural
    alerts, reactive metabolites, and protein cova-
    lent binding: how reliable are these attributes
    as predictors of drug toxicity? Chem Biodivers
    6(11):2115–2137

  10. Benigni R, Bossa C, Tcheremenskaia O
    (2013) Nongenotoxic carcinogenicity of che-
    micals: mechanisms of action and early


262 Jing Lu et al.

Free download pdf