deletions | additions       diff --git a/paragraph_Docking_AutoDock_cite_Morris_2009__.tex b/paragraph_Docking_AutoDock_cite_Morris_2009__.tex  index ddaac42..95f6873 100644  --- a/paragraph_Docking_AutoDock_cite_Morris_2009__.tex  +++ b/paragraph_Docking_AutoDock_cite_Morris_2009__.tex 
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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.  RF-Score \cite{Li_2015,Ballester_2010} uses a random forest classifier to score protein-ligand poses.  smina \cite{Koes_2013} is a fork of AutoDock Vina designed to better support energy minimization and custom scoring function development (scoring function terms and atom type properties can be specified using a run-time configuration file). It also simplifies the process of setting up a docking run with flexible sidechains.  VinaLC \cite{Zhang_2013} is a fork of AutoDock Vina designed to run on a cluster of multiprocessor machines. 
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PAPCA (PocketAnalyzerPCA) is a pocket detection utility designed to analyze ensembles of protein conformations.  PCS (Pocket Cavity Search) measures the volume of internal cavities and evaluates the environment of ionizable residues.  POVME (POcket Volume MEasurer) \cite{Durrant_2014} is tool for measuring and characterizing pocket volumes that includes a graphical user interface.