Journal of Medicinal Chemistry· 2012Q1
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
- 2,430citations
- Q1SCImago
- 2012year
Short summary
The Directory of Useful Decoys, Enhanced (DUD-E) offers an improved benchmarking set for molecular docking, featuring 102 diverse protein targets and 22,886 clustered ligands from ChEMBL, each with 50 property-matched decoys from ZINC.
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Key points
- DUD-E introduces an improved benchmarking set for molecular docking with 102 diverse protein targets.
- The set comprises 22,886 clustered ligands from ChEMBL, each paired with 50 property-matched decoys from ZINC.
- Decoy selection considers net charge and topological dissimilarity to ligands.
- An automated online tool is available for generating matched decoys for user-supplied ligands.
- DUD-E was used to enhance the balance of ligand desolvation and electrostatics in DOCK 3.6.
AI-generated from the title and abstract; the full text is not read.
Abstract
A key metric to assess molecular docking remains ligand enrichment against challenging decoys. Whereas the directory of useful decoys (DUD) has been widely used, clear areas for optimization have emerged. Here we describe an improved benchmarking set that includes more diverse targets such as GPCRs and ion channels, totaling 102 proteins with 22886 clustered ligands drawn from ChEMBL, each with 50 property-matched decoys drawn from ZINC. To ensure chemotype diversity, we cluster each target's ligands by their Bemis-Murcko atomic frameworks. We add net charge to the matched physicochemical properties and include only the most dissimilar decoys, by topology, from the ligands. An online automated tool (http://decoys.docking.org) generates these improved matched decoys for user-supplied ligands. We test this data set by docking all 102 targets, using the results to improve the balance between ligand desolvation and electrostatics in DOCK 3.6. The complete DUD-E benchmarking set is freely available at http://dude.docking.org.
The authors' abstract, as published at the source. Journal of Medicinal Chemistry, 2012 · DOI ↗
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Field: Computational Theory and Mathematics
Computational Theory and MathematicsComputer Science