subsection_Ligand_Based_Table_ref__.tex

\subsection*{Ligand-Based (Table~\ref{ligandtable})}

ACPC (AutoCorrelation of Partial Charges) \cite{Berenger_2014} computes ligand similarity based on a rotation and translation invariant electrostatic descriptor.

Align-it\textsuperscript{TM} is a successor of Pharao \cite{Taminau_2008} and aligns and scores 3D representations of molecules based on their pharmacophore features.  It includes a plugin for integration with PyMOL.

Open3DALIGN \cite{Tosco_2011} performs unsupervised rigid-body molecular alignment.

PAPER \cite{Haque_2010} performs GPU accelerated alignment of molecular shapes using Gaussian overlays.

Pharmer \cite{Koes_2011} uses efficient data structures to rapidly screen large libraries for ligand conformations that match a pharmacophore.

Pharmit \cite{Sunseri_2016} is a successor of Pharmer that also incorporates shape matching and energy minimization (if a receptor structure is available) as part of the screen.  It is primarily intended to be used as a backend to a web service.

Shape-it\textsuperscript{TM} uses Gaussian volumes to align and score molecular shapes.

USRCAT \cite{Schreyer_2012} performs ``ultra-fast shape recognition'' with the addition of pharmacophoric information to rapidly screen compound libraries for similar molecules.