Journal
PROTEIN SCIENCE
Volume 29, Issue 1, Pages 298-305Publisher
WILEY
DOI: 10.1002/pro.3784
Keywords
affinity ranking; cross-docking; docking; drug discovery; pose prediction; small molecule; virtual screening
Categories
Funding
- National Institutes of Health [GM097082, T32EB009403]
- Department of Defense
- NSF REU program
- National Science Foundation [DBI-1263020]
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Significant efforts have been devoted in the last decade to improving molecular docking techniques to predict both accurate binding poses and ranking affinities. Some shortcomings in the field are the limited number of standard methods for measuring docking success and the availability of widely accepted standard data sets for use as benchmarks in comparing different docking algorithms throughout the field. In order to address these issues, we have created a Cross-Docking Benchmark server. The server is a versatile cross-docking data set containing 4,399 protein-ligand complexes across 95 protein targets intended to serve as benchmark set and gold standard for state-of-the-art pose and ranking prediction in easy, medium, hard, or very hard docking targets. The benchmark along with a customizable cross-docking data set generation tool is available at . We further demonstrate the potential uses of the server in questions outside of basic benchmarking such as the selection of the ideal docking reference structure.
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