title: JADOPPT: java based AutoDock preparing and processing tool.
abstract: AutoDock is a very popular software package for docking and virtual screening. However, currently it is hard work to visualize more than one result from the virtual screening at a time. To overcome this limitation we have designed JADOPPT, a tool for automatically preparing and processing multiple ligand-protein docked poses obtained from AutoDock. It allows the simultaneous visual assessment and comparison of multiple poses through clustering methods. Moreover, it permits the representation of reference ligands with known binding modes, binding site residues, highly scoring regions for the ligand, and the calculated binding energy of the best ranked results.
  
  
  
  JADOPPT, supplementary material (Case Studies 1 and 2) and video tutorials are available at http://visualanalytics.land/cgarcia/JADOPPT.html.
  
  
  
  carlosgarcia@usal.es or pelaez@usal.es.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Mexico.|Departmento de Informática y Automática.
authors: Carlos
authors: C
authors: García-Pérez
authors: Quimica Farmacéutica.|Instituto de Investigación Biomédica de Salamanca (IBSAL).|Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Salamanca, Spain.
authors: Rafael
authors: R
authors: Peláez
authors: Departmento de Informática y Automática.
authors: Roberto
authors: R
authors: Therón
authors: Quimica Farmacéutica.
authors: José
authors: J
authors: Luis López-Pérez
mesh_terms: D000818:Animals; D001665:Binding Sites; D016000:Cluster Analysis; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins