David Koes edited AutoDock_cite_Morris_2009_is_an__.tex  about 8 years ago

Commit id: 55a6031d729a8e7ac55047e3a15621bc45420d07

deletions | additions      

       

MOLA \cite{Abreu_2010} is a pre-packaged distribution of AutoDock and AutoDock Vina for deployment on multi-platform computing clusters.  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.  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.