title: jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework.
abstract: BACKGROUND
  Molecular docking is a method for structure-based drug design and structural molecular biology, which attempts to predict the position and orientation of a small molecule (ligand) in relation to a protein (receptor) to produce a stable complex with a minimum binding energy. One of the most widely used software packages for this purpose is AutoDock, which incorporates three metaheuristic techniques. We propose the integration of AutoDock with jMetalCpp, an optimization framework, thereby providing both single- and multi-objective algorithms that can be used to effectively solve docking problems.
  
  
  RESULTS
  The resulting combination of AutoDock + jMetalCpp allows users of the former to easily use the metaheuristics provided by the latter. In this way, biologists have at their disposal a richer set of optimization techniques than those already provided in AutoDock. Moreover, designers of metaheuristic techniques can use molecular docking for case studies, which can lead to more efficient algorithms oriented to solving the target problems.
  
  
  METHODS
  jMetalCpp software adapted to AutoDock is freely available as a C++ source code at http://khaos.uma.es/AutodockjMetal/.
authors.affiliation: Lenguajes y Ciencias de la Computación, Universidad de Málaga, Bulevar Louis Pasteur 35, 29071, Málaga, Spain.
authors.forename: Esteban
authors.initials: E
authors.lastname: López-Camacho
authors.forename: María Jesús
authors.initials: MJ
authors.lastname: García Godoy
authors.forename: Antonio J
authors.initials: AJ
authors.lastname: Nebro
authors.forename: José F
authors.initials: JF
authors.lastname: Aldana-Montes
mesh_terms: D000465:Algorithms; D015195:Drug Design; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins