title: Building a virtual ligand screening pipeline using free software: a survey.
abstract: Virtual screening, the search for bioactive compounds via computational methods, provides a wide range of opportunities to speed up drug development and reduce the associated risks and costs. While virtual screening is already a standard practice in pharmaceutical companies, its applications in preclinical academic research still remain under-exploited, in spite of an increasing availability of dedicated free databases and software tools. In this survey, an overview of recent developments in this field is presented, focusing on free software and data repositories for screening as alternatives to their commercial counterparts, and outlining how available resources can be interlinked into a comprehensive virtual screening pipeline using typical academic computing facilities. Finally, to facilitate the set-up of corresponding pipelines, a downloadable software system is provided, using platform virtualization to integrate pre-installed screening tools and scripts for reproducible application across different operating systems.
authors.forename: Enrico
authors.initials: E
authors.lastname: Glaab
mesh_terms: D000465:Algorithms; D055808:Drug Discovery / Q000379:methods*; D057166:High-Throughput Screening Assays / Q000379:methods; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D008024:Ligands
keywords: ADMETox; docking; off-target effects; protein–ligand binding; virtual screening; workflow management