title: NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID.
abstract: Ligand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chains and definition of geometric constraints. Furthermore, the NRGsuite permits the visualization of the docking simulation in real time. The NRGsuite give access to powerful docking simulations that can be used in structure-guided drug design as well as an educational tool. The NRGsuite is implemented in Python and C/C++ with an easy to use package installer. The NRGsuite is available for Windows, Linux and MacOS.
  
  
  METHODS
  http://bcb.med.usherbrooke.ca/flexaid.
  
  
  BACKGROUND
  rafael.najmanovich@usherbroke.ca.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada.
authors.forename: Francis
authors.initials: F
authors.lastname: Gaudreault
authors.affiliation: Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada.
authors.forename: Louis-Philippe
authors.initials: LP
authors.lastname: Morency
authors.affiliation: Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada.
authors.forename: Rafael J
authors.initials: RJ
authors.lastname: Najmanovich
mesh_terms: D001665:Binding Sites; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins