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icons/,\ | ||
data/,\ | ||
html/,\ | ||
toc.xml | ||
tocEP.xml,\ | ||
tocModels.xml |
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> | ||
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<html> | ||
<head> | ||
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> | ||
<title>AhR Models</title> | ||
<link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css"> | ||
</head> | ||
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<body> | ||
<h1>AhR Models</h1> | ||
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<h2>Data source</h2> | ||
Data originates from the <a href="http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=2796&loc=ea_ras">PubChem BioAssay 2796</a>, | ||
named <i>Luminescence-based cell-based high throughput confirmation assay for activators of the Aryl Hydrocarbon Receptor</i>. | ||
The data was filtered for unknown CDK atom types, | ||
and contained after this filtering 15951 compounds where | ||
7971 were annotated as <i>Active</i>, and 7980 compounds as <i>Inactive</i>. | ||
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<h2>Models</h2> | ||
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<table> | ||
<td bgcolor="cccccc" width=150>Model type</td> | ||
<td bgcolor="cccccc">Model implementation</td> | ||
<td bgcolor="cccccc">Comment</td> | ||
<tr> | ||
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<td>Exact Match</td> | ||
<td>Molecular Signature</td> | ||
<td></td> | ||
<tr> | ||
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<td>Near Neighbor</td> | ||
<td>CDK Fingerprint</td> | ||
<td>Tanimoto distance > 0.7</td> | ||
<tr> | ||
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<td>Structural alerts</td> | ||
<td>Signatures</td> | ||
<td></td> | ||
<tr> | ||
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<td>QSAR</td> | ||
<td>SVM model with Signature descriptor height 0-3</td> | ||
<td></td> | ||
<tr> | ||
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</table> | ||
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</body> | ||
</html> |
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<?xml version="1.0" encoding="UTF-8"?> | ||
<?NLS TYPE="org.eclipse.help.toc"?> | ||
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<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedModels" label="AhR" > | ||
<topic label="AhR" href="html/ahrmodels.html" /> | ||
</toc> |
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data/,\ | ||
html/,\ | ||
icons/,\ | ||
toc.xml,\ | ||
models/ | ||
tocModels.xml,\ | ||
models/,\ | ||
tocEP.xml |
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> | ||
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<html> | ||
<head> | ||
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> | ||
<title>Ames Mutagenicity Models</title> | ||
<link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css"> | ||
</head> | ||
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<body> | ||
<h1>Ames Mutagenicity Models</h1> | ||
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<h2>Overview</h2> | ||
These mutagenicity models are built on data from Ames <i>Salmonella</i> microsome mutagenicity assays | ||
(AMES test) [1]. | ||
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<h2>Data source</h2> | ||
The AMES dataset published by Kazius et al. [2] was downloaded from | ||
<a href="http://cheminformatics.org/datasets/bursi/"> | ||
http://cheminformatics.org/datasets/bursi/</a>. | ||
The dataset contained 4337 chemical structures of which 2401 were | ||
classified as <i>mutagen</i>, and 1936 <i>nonmutagen</i>. | ||
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<h2>Models</h2> | ||
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<table> | ||
<td bgcolor="cccccc" width=150>Model type</td> | ||
<td bgcolor="cccccc">Model implementation</td> | ||
<td bgcolor="cccccc">Comment</td> | ||
<tr> | ||
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<td>Exact Match</td> | ||
<td>Molecular Signature</td> | ||
<td></td> | ||
<tr> | ||
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<td>Near Neighbor</td> | ||
<td>CDK Fingerprint</td> | ||
<td>Tanimoto distance > 0.7</td> | ||
<tr> | ||
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<td>Structural alerts</td> | ||
<td>SMARTS</td> | ||
<td>List of SMARTS defined in [2]</td> | ||
<tr> | ||
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<td>QSAR</td> | ||
<td>SVM model with Signature descriptor height 0-3</td> | ||
<td></td> | ||
<tr> | ||
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</table> | ||
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<h2>References</h2> | ||
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[1] K. Mortelmans and E. Zeiger<br> | ||
The ames salmonella/microsome mutagenicity assay<br> | ||
<i>Mutat Res</i>, 455(1-2):29-60, Nov 2000<br> | ||
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<p> | ||
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[2] J. Kazius, R. McGuire, and R. Bursi<br> | ||
Derivation and validation of toxicophores for mutagenicity prediction<br> | ||
<i>J Med Chem</i>, 48(1):312-320, Jan 2005<br> | ||
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</body> | ||
</html> |
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4 changes: 2 additions & 2 deletions
4
plugins/net.bioclipse.ds.models.ames/toc.xml → ...ns/net.bioclipse.ds.models.ames/tocEP.xml
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<?xml version="1.0" encoding="UTF-8"?> | ||
<?NLS TYPE="org.eclipse.help.toc"?> | ||
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<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedEndpoints" label="Mutagenicity EP" > | ||
<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedEndpoints" label="Mutagenicity" > | ||
<topic label="Mutagenicity" href="html/mutagenicity.html" /> | ||
</toc> | ||
</toc> |
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<?xml version="1.0" encoding="UTF-8"?> | ||
<?NLS TYPE="org.eclipse.help.toc"?> | ||
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<toc link_to="../net.bioclipse.ds.ui/toc.xml#ContributedModels" label="Ames Mutagenicity" > | ||
<topic label="Ames Mutagenicity" href="html/ames.html" /> | ||
</toc> |
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@@ -5,4 +5,5 @@ bin.includes = META-INF/,\ | |
plugin.xml,\ | ||
data/,\ | ||
html/,\ | ||
toc.xml | ||
tocEP.xml,\ | ||
tocModels.xml |
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plugins/net.bioclipse.ds.models.daphnia/html/aquatictox.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> | ||
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<html> | ||
<head> | ||
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> | ||
<title>Aquatic Toxicity</title> | ||
<link rel="stylesheet" href="../../PRODUCT_PLUGIN/narrow_book.css" type="text/css"> | ||
</head> | ||
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<body> | ||
<h1>Aquatic Toxicity</h1> | ||
<a href="http://en.wikipedia.org/wiki/Aquatic_toxicology">Aquatic toxicology</a> is the study of the effects of manufactured chemicals on aquatic organisms. | ||
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<p> | ||
<h2>Daphnid assay</h2> | ||
<a href="http://en.wikipedia.org/wiki/Daphnia">Daphnia</a> are small, planktonic crustaceans widely used in aquatic toxicity testing. | ||
A list of structural alerts (SMARTS) consiting of 18 manually created SMARTS from the publication below was kindly supported by Emma Schymanski. | ||
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<p> | ||
<h2>References</h2> | ||
Peter C. von der Ohe, Ralph Kühne,Ralf-Uwe Ebert, Rolf Altenburger, Matthias Liess, and Gerrit Schüürmann<br> | ||
<a href="http://pubs.acs.org/doi/abs/10.1021/tx0497954">Structural Alerts: A New Classification Model to Discriminate Excess Toxicity from Narcotic Effect Levels of Organic Compounds in the Acute Daphnid Assay</a><br> | ||
<i>Chemical Research in Toxicology</i> 2005 18 (3), 536-555<br> | ||
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</body> | ||
</html> |
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