deletions | additions
diff --git a/subsection_Descriptor_Calculators_Table_ref__.tex b/subsection_Descriptor_Calculators_Table_ref__.tex
index 0a4c35f..61e644c 100644
--- a/subsection_Descriptor_Calculators_Table_ref__.tex
+++ b/subsection_Descriptor_Calculators_Table_ref__.tex
...
\subsection*{Model Building (Table~\ref{qsarmodel})}
AZOrange \cite{St_lring_2011} is a machine learning package that supports QSAR model building in a full work flow from descriptor computation to automated model building, validation and selection. It promotes model accuracy by using several high performance machine learning algorithms for efficient data set specific selection of the statistical approach.
Bioalerts \cite{Cortes_Ciriano_2016} uses RDKit
fingerprint fingerprints to create models from discrete (e.g., toxic/non-toxic) and continuous data. It includes the capability to visualize problematic functional groups.
Chemistry aware model builder (camb) \cite{Murrell_2015} is an R package for the generation of quantitative models. Its
features capabilities include descriptor calculation (including 905 two-dimensional and 14 fingerprint type descriptors for small molecules, 13 whole protein sequence descriptors, and 8 types of amino acid descriptors), model generation, ensemble modeling, and
visualization (With ggplot2). visualization.
eTOXLab \cite{Carri__2015} provides a portable modeling framework embedded in a self-contained virtual machine for easy deployment.
Open3DGrid and Open3DQSAR \cite{Tosco_2010} are a suite of related tools that
aid in developed build 3D QSAR models. Open3DGrid generates molecular interaction fields (MIFs) in a variety of formats, and Open3DQSAR builds predictive models from the MIFs of aligned molecules. Calculations can be visualized in real time in PyMOL.
QSAR-tools is a set of Python scripts that use RDKit to
model quantitative structure activity relationships build linear QSAR models from 2D chemical data.
It inputs SMILES file of a training set and computes a set of smarts descriptors unique to that set. By using a fingerprint file, it trains a linear model to predict a numerical quantity of interest and is capable of mapping the model onto the compound to produce an image.
\paragraph{Model \subsection*{Model Application (Table~\ref{qsarapply})}
SMARTCyp \cite{Rydberg_2010} is a QSAR model that predicts the sites of cytochrome P450-mediated metabolism of
drug like drug-like molecules directly from the 2D structure of a molecule using
fragment based fragment-based energy rules.
Toxtree \cite{Patlewicz_2008} is a Java GUI application for estimating the ``toxic hazard'' of molecules using a variety of toxicity prediction modules, such as oral toxicity, skin and eye irritation prediction, covalent protein binding and DNA binding, Cytochrome P450-mediated drug metabolism (using SMARTCyp) and more.
UG-RNN/AquaSol \cite{Lusci_2013} is an undirected graph recursive neural network that has been trained to predict aqueous solubility from molecular graphs.
\paragraph{Visualization \subsection*{Visualization (Table~\ref{qsarviz})}
CheS-Mapper (chemical space mapper) \cite{G_tlein_2012,G_tlein_2014}. is a 3D-viewer for small compounds in chemical datasets. It embeds a dataset into 3D space
in such a way that the relationship between by performing dimensionality reduction on the
structure of chemical compounds, their physico-chemical properties, and biological or toxic effects can be analyzed. In chemical space, compounds that have similar descriptor values places close to each other. CheS-Mapper can calculate variety properties of
descriptors and supports clustering and 3D alignment the compounds.
DataWarrior \cite{Sander_2015} is a data visualization and analysis tool for chemical data with a rich set of available property calculations, similarity metrics, modeling capabilities, and data set representations.
DecoyFinder \cite{Cereto_Massague_2012} provides a GUI
for selecting a set of decoy compounds from a large library that are appropriate matches to a given set of actives.
Scaffold Hunter \cite{Wetzel_2009} provides a Java-based GUI for visualizing the relationship between compounds in a dataset.
Synergy Maps \cite{Lewis_2015} visualizes synergistic activity extracted from screens of drug combinations.
VIDEAN (visual and interactive descriptor analysis) \cite{Mart_nez_2015} is a visual tool for
iteratively choosing a subset of descriptors appropriate for predicting a target property with
the aid of statistical methods.
Descriptor selection and model building are performed iteratively at the direction of the user.
WCSE (Wikipedia chemical structure explorer) \cite{Ertl_2015} runs as a web application and provides a 2D interface for visualizing and searching for 2D molecules.
