OSPREY is a suite of programs for computational structure-based protein design. OSPREY is developed in the lab of Prof. Bruce Donald at Duke University. OSPREY 3.0 offers a unique package of advantages over other design software, including provable design algorithms that account for continuous flexibility during design and model conformational. OSPREY has been used for an impressive number of empirically successful designs, ranging from enzyme design to antibody design to prediction of antibiotic resistance mutations. OSPREY 3.0 is available at http://www.cs.duke.edu/donaldlab/osprey.php as free and open-source software.

1. Biological Sciences faculty
Biophysics Department
OSPREY: Open-Source Protein REdesign for You
Presented By
Alireza Doustmohammadi
Graduate Student in Bioinformatics
May 2020
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2. Contents
Introduction
OSPREY Pipeline
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OSPREY3 vs OSPREY 2
Accuracy Benchmarks

3. Introduction
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OSPREY:
[https://users.cs.duke.edu/]
a suite of programs for
computational structure-based
protein design.
OSPREY Tarbiat Modares University

4. Introduction
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OSPREY:
Open Source Software
OSPREY Tarbiat Modares University

5. PipelineInput Structure
How OSPREY work
OSPREY
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Energy Parameters
OSPREY Tarbiat Modares University
Input
Structure
Rotamer
Libraries
Energy
Function
Configurations
Energy Minimization
OSPREY can run on GPU
import osprey
osprey.start()
FlexibilityComputation

6. PipelineInput Structure
OSPREY Input Structure
OSPREY
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• Add All Hydrogens
• Swap Heteroatom
• Remove extra atoms
Energy ParametersFlexibilityComputation
[http://molprobity.biochem.duke.edu/] [http://www.yasara.org/]

7. PipelineInput Structure
Choose Force field
OSPREY
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Energy Parameters
• AMBER
• CHARMM22
• CHARMM19NEUTRAL
• CHARMM19
ffparams = osprey.ForcefieldParams(osprey.Forcefield.AMBER)
We can use Custom Template Library
FlexibilityComputation

8. PipelineInput Structure
Protein Flexibility
OSPREY
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Energy ParametersFlexibilityComputation

9. PipelineInput Structure
Complex Protein Flexibility
OSPREY
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Energy ParametersFlexibilityComputation

10. PipelineInput Structure
Compute Energy
OSPREY
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Energy ParametersFlexibilityComputation

11. PipelineInput Structure
Parallel Compute Energy
OSPREY
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Energy ParametersFlexibilityComputation
parallelism = osprey.Parallelism(cpuCores=2, gpus=1, streamsPerGpu=1)

12. PipelineInput Structure
Parallel Compute Energy
OSPREY
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Energy ParametersFlexibilityComputation
parallelism = osprey.Parallelism(cpuCores=2, gpus=1, streamsPerGpu=1)

13. OSPREY3 vs OSPREY 2
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[Hallen, M. A., Martin, J. W., Ojewole, A., Jou, J. D., Lowegard, A. U., Frenkel, M. S., Gainza, P., Nisonoff, H. M., Mukund, A.,
Wang, S., Holt, G. T., Zhou, D., Dowd, E., Donald, B. R.. J. Comput. Chem. 2018, 39, 2494– 2507. 10.1002/jcc.25522]

14. OSPREY3 vs OSPREY 2
14 of 15OSPREY Tarbiat Modares University
[Hallen, M. A., Martin, J. W., Ojewole, A., Jou, J. D., Lowegard, A. U., Frenkel, M. S., Gainza, P., Nisonoff, H. M., Mukund, A.,
Wang, S., Holt, G. T., Zhou, D., Dowd, E., Donald, B. R.. J. Comput. Chem. 2018, 39, 2494– 2507. 10.1002/jcc.25522]

15. Accuracy Benchmarks
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[Hallen, M. A., Martin, J. W., Ojewole, A., Jou, J. D., Lowegard, A. U., Frenkel, M. S., Gainza, P., Nisonoff, H. M., Mukund, A.,
Wang, S., Holt, G. T., Zhou, D., Dowd, E., Donald, B. R.. J. Comput. Chem. 2018, 39, 2494– 2507. 10.1002/jcc.25522]