Assessing and improving the performance of consensus docking strategies using the DockBox package.
Jordane Preto1,2, Francesco Gentile3,4
1Department of Oncology, University of Alberta, Edmonton, AB, Canada. jordane.preto@univ-lyon1.fr.
Journal of Computer-Aided Molecular Design
|October 4, 2019
Summary
DockBox software improves molecular docking accuracy using a novel score-based consensus docking (SBCD) method. SBCD enhances drug discovery by increasing hit rates in virtual screening with minimal computational cost.
Area of Science:
- Computational chemistry
- Drug discovery
- Bioinformatics
Background:
- Molecular docking predicts ligand-protein binding and binding strength, crucial for drug discovery.
- Selecting optimal docking programs for specific targets remains challenging.
- Existing consensus methods can be computationally intensive or limited in scoring function flexibility.
Purpose of the Study:
- Introduce DockBox, a package for utilizing multiple docking and scoring programs with consensus strategies.
- Present Score-Based Consensus Docking (SBCD), a new consensus method within DockBox.
- Evaluate SBCD's performance in improving pose prediction and virtual screening efficacy.
Main Methods:
- Developed DockBox, an open-source computational package.
- Implemented SBCD, a novel consensus docking approach.
- Compared SBCD performance against single docking programs and standard consensus docking (CD).
Main Results:
- SBCD significantly improved pose prediction success rates compared to individual docking programs.
- SBCD enhanced enrichment factors and hit rates in virtual screening over standard CD.
- SBCD offers minimal additional computational cost and time compared to CD when using the same docking programs.
- SBCD efficiently integrates multiple scoring functions for consensus assessment.
Conclusions:
- DockBox and its SBCD method offer a powerful, efficient, and flexible approach for molecular docking.
- SBCD shows significant improvements in accuracy and hit identification for virtual screening.
- The open-source DockBox package facilitates advanced computational drug discovery efforts.
Keywords:
Binding pose predictionComputer-aided drug discoveryConsensus dockingDocking softwareScoring functionsVirtual screeningMore Related Videos
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