deletions | additions       diff --git a/paragraph_Docking_AutoDock_cite_Morris_2009__.tex b/paragraph_Docking_AutoDock_cite_Morris_2009__.tex  index 95f6873..0d85a43 100644  --- a/paragraph_Docking_AutoDock_cite_Morris_2009__.tex  +++ b/paragraph_Docking_AutoDock_cite_Morris_2009__.tex 
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MOLA \cite{Abreu_2010} is a pre-packaged distribution of AutoDock and AutoDock Vina for deployment on multi-platform computing clusters.  Paradocks \cite{Meier_2010} is a parallelized docking program that includes a number of population-based metaheuristics, such as particle swarm optimization, for exploring the  PyRx \cite{Dallakyan_2014} is a visual interface for AutoDock and AutoDock Vina that simplifies setting up and analyzing docking workflows. Its future as an open-source solution is in doubt due to a recent shift to commercialization.  rDock \cite{Ruiz_Carmona_2014} is designed for docking against proteins or nucleic acids and can incorporate user-specified constraints. It uses an empirical scoring function that includes solvent accessible surface area terms. A combination of genetic algorithms, Monte Carlo, and simplex minimization is used to explore the conformational space. Distinct scoring functions are provided for docking to proteins and nucleic acids. 
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VinaLC \cite{Zhang_2013} is a fork of AutoDock Vina designed to run on a cluster of multiprocessor machines.  VinaMPI \cite{Ellingson_2013} is a wrapper for AutoDock Vina that uses OpenMPI to run large-scale virtual screens on a computing cluster.  \paragraph{Pocket Detection}  fpocket \cite{Schmidtke_2011} detects and delineates protein cavities using Voronoi tessellation and is able to process molecular dynamics simulations.