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HybridSim-VS: a web server for large-scale ligand-based virtual screening using hybrid similarity recognition
Jinling Shang1, Xi Dai1, Yecheng Li1
1School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China.
Bioinformatics (Oxford, England)
|October 17, 2017
Summary
A new HybridSim method combines 2D fingerprint and 3D shape similarity searches for improved virtual screening (VS) in drug discovery. This approach enhances performance over individual methods and powers the HybridSim-VS online platform for large-scale compound screening.
Area of Science:
- Computational chemistry and cheminformatics
- Drug discovery and development
- Bioinformatics and computational biology
Background:
- Ligand-based virtual screening (VS) commonly employs 2D fingerprint and 3D shape similarity methods.
- These methods have distinct advantages but are often used independently in drug discovery.
- There is a need to integrate these approaches for more effective VS.
Purpose of the Study:
- To develop and evaluate a general hybrid molecular-similarity protocol (HybridSim) combining 2D fingerprint and 3D shape VS methods.
- To assess the performance of HybridSim against individual 2D and 3D methods.
- To create an accessible online platform (HybridSim-VS) for large-scale virtual screening.
Main Methods:
- Developed the HybridSim protocol by merging 2D fingerprint and 3D shape similarity search techniques.
- Evaluated HybridSim performance using 595,036 actives and decoys across 40 targets from the Directory of Useful Decoys Enhanced (DUD-E) dataset.
- Implemented the HybridSim method into the HybridSim-VS web server, incorporating 17,839,945 screenable compounds.
Main Results:
- HybridSim demonstrated significantly improved overall performance in virtual screening across 40 projects compared to using only 2D fingerprint or 3D shape methods.
- The HybridSim-VS platform offers large-scale and proficient virtual screening capabilities.
- The study provides a robust method for enhancing ligand-based virtual screening.
Conclusions:
- Hybridizing 2D fingerprint and 3D shape similarity methods offers a superior approach for ligand-based virtual screening.
- The developed HybridSim protocol and its associated web server (HybridSim-VS) provide valuable tools for drug discovery.
- This integrated approach enhances the efficiency and effectiveness of identifying potential drug candidates.
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