title: RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening.
abstract: CONCLUSIONS
  Evaluation of the capacity for separating actives from challenging decoys is a crucial metric of performance related to molecular docking or a virtual screening workflow. The Directory of Useful Decoys (DUD) and its enhanced version (DUD-E) provide a benchmark for molecular docking, although they only contain a limited set of decoys for limited targets. DecoyFinder was released to compensate the limitations of DUD or DUD-E for building target-specific decoy sets. However, desirable query template design, generation of multiple decoy sets of similar quality, and computational speed remain bottlenecks, particularly when the numbers of queried actives and retrieved decoys increases to hundreds or more. Here, we developed a program suite called RApid DEcoy Retriever (RADER) to facilitate the decoy-based assessment of virtual screening. This program adopts a novel database-management regime that supports rapid and large-scale retrieval of decoys, enables high portability of databases, and provides multifaceted options for designing initial query templates from a large number of active ligands and generating subtle decoy sets. RADER provides two operational modes: as a command-line tool and on a web server. Validation of the performance and efficiency of RADER was also conducted and is described.
  
  
  METHODS
  RADER web server and a local version are freely available at http://rcidm.org/rader/ .
  
  
  BACKGROUND
  lingwang@scut.edu.cn or went@scut.edu.cn .
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Pre-Incubator for Innovative Drugs & Medicine, School of Bioscience and Bioengineering, South China University of Technology, 382 East Circle at Higher Education Mega Center, Guangzhou 510006, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Wang
authors.affiliation: Pre-Incubator for Innovative Drugs & Medicine, School of Bioscience and Bioengineering, South China University of Technology, 382 East Circle at Higher Education Mega Center, Guangzhou 510006, China.
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Pang
authors.affiliation: Pre-Incubator for Innovative Drugs & Medicine, School of Bioscience and Bioengineering, South China University of Technology, 382 East Circle at Higher Education Mega Center, Guangzhou 510006, China.
authors.forename: Yecheng
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
authors.forename: Ziying
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Pre-Incubator for Innovative Drugs & Medicine, School of Bioscience and Bioengineering, South China University of Technology, 382 East Circle at Higher Education Mega Center, Guangzhou 510006, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Tan
mesh_terms: D062126:Databases, Chemical; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D012984:Software
chemical_list: D008024:Ligands