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DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and
Alberto Cuzzolin1, Mattia Sturlese2, Ivana Malvacio3
1Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy. antonella.ciancetta@unipd.it.
DockBench 1.0 simplifies virtual screening (VS) by automating docking benchmarks and setup. This platform enhances drug discovery by streamlining computational methods for identifying potential drug candidates.
Area of Science:
- Computational chemistry
- Drug discovery
- Bioinformatics
Background:
- Virtual screening (VS) accelerates drug discovery by computationally identifying potential drug candidates.
- Structure-based VS (SBVS) uses protein 3D structures and docking to find novel drug hits.
- Accurate docking protocols are critical for successful SBVS, but benchmarking is complex.
Purpose of the Study:
- To present DockBench 1.0, a free platform for automating docking benchmarks and virtual screening (VS) setups.
- To simplify the process of selecting optimal docking protocols for SBVS experiments.
- To validate the platform through a benchmark study of human Checkpoint kinase 1 (hChk1).
Main Methods:
- DockBench 1.0 automates the entire pipeline from docking benchmark to VS setup.
- The platform supports seven docking software packages and seventeen different protocols.
- A benchmark study of human Checkpoint kinase 1 (hChk1) was conducted for validation.
Main Results:
- DockBench 1.0 successfully automates the benchmarking and setup of virtual screening protocols.
- The platform integrates multiple docking software and protocols, simplifying complex workflows.
- Validation using hChk1 demonstrates the platform's utility in selecting effective docking strategies.
Conclusions:
- DockBench 1.0 significantly eases the setup of structure-based virtual screening campaigns.
- Automating docking benchmarks reduces the complexity and resource requirements for drug discovery.
- The platform provides a valuable tool for researchers seeking to optimize VS protocols.
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