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OSPREY 3.0: Open-source protein redesign for you, with powerful new features
Mark A Hallen1,2, Jeffrey W Martin1, Adegoke Ojewole3
1Department of Computer Science, Duke University, Durham, North Carolina, 27708.
Journal of Computational Chemistry
|October 29, 2018
Summary
Osprey 3.0, a new protein design software, offers significant speedups and enhanced biophysical modeling. This improved tool accurately predicts mutation effects on protein binding, aiding researchers in protein engineering.
Area of Science:
- Computational Biology
- Biophysics
- Software Engineering
Background:
- Protein design software is crucial for advancing biotechnology and drug discovery.
- Previous versions of Osprey provided valuable tools for protein engineering.
- There is a continuous need for faster and more accurate protein design algorithms.
Purpose of the Study:
- To introduce Osprey 3.0, a substantially improved release of the Osprey protein design software.
- To highlight the new features, performance enhancements, and improved modeling capabilities of Osprey 3.0.
- To demonstrate the software's accuracy in predicting mutation effects on protein-protein binding.
Main Methods:
- Development of a new Python interface for improved usability.
- Implementation of new algorithms for speed and enhanced biophysical modeling.
- Integration of GPU support for significant performance acceleration.
Main Results:
- Osprey 3.0 achieves speedups of over two orders of magnitude compared to previous versions.
- New algorithms and GPU support provide substantial performance gains.
- Empirical validation confirms accurate prediction of mutation effects on protein-protein binding.
Conclusions:
- Osprey 3.0 represents a major advancement in protein design software.
- The software offers unique advantages, including provable algorithms and accurate conformational entropy modeling.
- Osprey 3.0 is available as free and open-source software, promoting accessibility in research.
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