subsection_Descriptor_Calculators_Table_ref__.tex

\subsection*{Descriptor Calculators (Table~\ref{descriptors})}
4D Flexible Atom-Pair Kernel (4D FAP) computes a `4D' similarity measure from the molecular graphs of an ensemble of conformations which can be incorporated into QSAR models.

The BlueDesc descriptor calculator is a command-line tool that converts an MDL SD file into ARFF and LIBSVM format using CDK and JOELib2 for machine learning and data mining purposes. It computes 174 descriptors taken from both libraries.

MolSig \cite{Carbonell_2013} computes molecular graph descriptors that include stereochemistry information.

PaDEL-Descriptor  \cite{Yap_2010} calculates molecular descriptors and fingerprints. It computes 1875 descriptors (1444 1D, 2D descriptors and 431 3D descriptors) and 12 types of fingerprints. 

Topological maximum cross correlation descriptors (TMACC) \cite{Melville_2007} generates 2D autocorrelation descriptors that are low dimensional and interpretable and appropriate for QSAR modeling.

\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 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 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.

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 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 build linear QSAR models from 2D chemical data. 

\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 molecules directly from the 2D structure of a molecule using 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. 

\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 by performing dimensionality reduction on the properties of 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.  

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.

WebChemViewer  \cite{Durrant_2014} is an online viewer for viewing and interacting with lists of compounds and their associated data.