Facilitates decoy based assessment of virtual screening. RADER adopts a 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. It can format and utilize large databases for future work and to append additional databases to the existing one at any time; select unique and diverse compounds as queries from a large number of active ligands, and then generate subtle decoy sets. Therefore, RADER provides a fast, versatile, and user-friendly method to automatically create tailor-made decoy sets for any given sets of bioactives.

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RADER classification

RADER specifications

Software type:
Package
Restrictions to use:
None
Input format:
SMILES, PDB, SDF, MOL, MOL2
Output format:
SDF, SMI
Computer skills:
Advanced
Interface:
Command line interface
Input data:
Selects unique and diverse compounds as queries from a large number of active ligands.
Output data:
Generates subtle decoy sets.
Operating system:
Unix/Linux, Mac OS, Windows
Stability:
Stable

User report

0 user reviews

0 user reviews

No review has been posted.

RADER forum

No open topic.

RADER classification

RADER specifications

Software type:
Package
Restrictions to use:
None
Input format:
SMILES, PDB, SDF, MOL, MOL2
Output format:
SDF, SMI
Stability:
Stable
Interface:
Web user interface
Input data:
Selects unique and diverse compounds as queries from a large number of active ligands.
Output data:
Generates subtle decoy sets.
Computer skills:
Basic
Source code URL:
http://rcidm.org/static/RADER.zip

Publications

  • (Wang et al., 2016) RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening. Bioinformatics.
    PMID: 28011765

Credits

Institution(s)

Pre-Incubator for Innovative Drugs & Medicine, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China; Yinfotech Inc., Guangzhou, China

Funding source(s)

This work was supported by the Science and Technology Planning Project of Guangdong Province (No. 2015B010109004), the National Natural Science Foundation of China (No. 81502984), the Natural Science Foundation of Guangdong Province (No. 2016A030310421), and the Fundamental Research Funds for the Central Universities (No. 2015ZM049).

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