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DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0
Xiaohui Jiang1, Kamal Kumar, Xin Hu
1Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA. xjiang@bioanalysis.org
Chemistry Central Journal
|September 10, 2008
Summary
DOVIS 2.0 enhances virtual screening by upgrading to AutoDock 4.0, improving efficiency, and standardizing output formats for drug discovery. This new version offers better performance and usability for researchers.
Area of Science:
- Computational chemistry
- Bioinformatics
- Drug discovery
Background:
- Small-molecule docking is crucial for understanding receptor-ligand interactions and identifying drug candidates.
- The original DOVIS software facilitated large-scale virtual screening using AutoDock 3.05 on Linux clusters.
- DOVIS enabled the screening of millions of compounds on high-performance computing platforms.
Purpose of the Study:
- To report significant advances in the DOVIS 2.0 software implementation.
- To enhance screening capability, improve file system efficiency, and extend usability.
- To upgrade the docking engine and optimize parallelization for improved performance.
Main Methods:
- Upgraded the docking engine to AutoDock 4.0.
- Developed a new parallelization scheme for improved runtime efficiency.
- Modified AutoDock code to reduce file operations and implemented sd-file format output.
- Created a wrapper-script interface for automated rescoring with third-party programs.
Main Results:
- DOVIS 2.0 demonstrates improved performance and usability over the previous version.
- Achieved highly efficient computation through automated load balancing.
- Reduced excessive file operations by over 95%.
- Standardized output to industry-standard sd-file format and enabled flexible ligand rescoring.
Conclusions:
- DOVIS 2.0 offers significant improvements in computational efficiency and user-friendliness for virtual screening.
- The software facilitates seamless integration with other modeling programs via sd-file output.
- DOVIS 2.0 is freely available under the GNU General Public License, promoting wider accessibility in research.
