RADER (RApid DEcoy Retriever)
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. 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 may NOT be used for commercial purposes.
If you use RADER, Please cite:
(1) Ling Wang, Xiaoqian Pang, Yecheng Li, Ziying Zhang, and Wen Tan. RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening. Bioinformatics 2016, DOI 10.1093/bioinformatics/btw783.
(2) Jinling Shang, Yecheng Li, Xiaoqian Pang, Ziying Zhang, and Ling Wang. Constructing benchmarking sets for targets in PI3K-AKT-mTOR pathway through RADER algorithm. J. Chem. Inf. Model. 2017, submitted.
- Archive compound database
- Design query templates
- Generate decoys
- Zinc (17,900,742)
- ChEMBL (1,583,897)
- BindingDB (545,659)
- GDB (50,000,000)
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