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Software Developed by the Donald Lab

Main OSPREY website: http://www.cs.duke.edu/donaldlab/osprey.php.

Other Versions of OSPREY

We have released the OSPREY code open-source following publication of our papers. In order to fully document the computational and experimental designs in our papers, we have made several builds of the OSPREY codebase available.

  1. For general redesign problems, we recommend using version 3 of OSPREY, which has improved features, user interface, and performance. It is available on our Github page.

  2. The previous release is OSPREY v2.2 beta , and the previous major release is OSPREY v2.0. Please see the license for OSPREY 2 and earlier if you wish to use these versions.

  3. If you wish to use the stable release before that, OSPREY v1.0 released in May 2009, you can download it here. We also have a separate user manual and a power point tutorial available for OSPREY v1.0. OSPREY v1.0 is consistent with the experiments described in:

      C. Chen, I. Georgiev, A. C. Anderson, and B. R. Donald. Computational structure-based redesign of enzyme activity. Proc Natl Acad Sci U S A. 106(10):3764-3769, 2009.

  4. Also, an alternative version of the OSPREY software is consistent with the K* computational experiments described in our 2010 PNAS paper:

      Frey KM, Georgiev I, Donald BR, Anderson AC. Predicting resistance mutations using protein design algorithms. Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13707-12. Epub 2010 Jul 19. PMID: 20643959
    That version of OSPREY can be downloaded here. There are several changes in the scripts for this version. K* uses both intra- and inter-mutation pruning as described in our Journal of Computational Chemistry (2008) paper. The intra- & inter-mutation pruning algorithms ensure provably-accurate K* scores for the best-scoring mutants and structures. This suffices for positive design, in which good-scoring structures and mutants are of interest.

    However for negative design, we are interested in poorly-scoring structures and mutants as well. For poorly-scoring structures and mutants the 2008 inter-mutation pruning algorithm does not guarantee accurate scores. For this reason, some modifications were undertaken to extend the algorithm for provably-accurate negative design. Specifically, either changing `gamma' (which controls the inter-mutation pruning fraction) or disabling the inter-mutation pruning may be necessary for provably-accurate negative design. These changes are described in the version provided here. For our study published in PNAS (2010), we tried both ways. In practice we have found that the negative design predictions are often still adequate even with the inter-mutation pruning enabled.

  5. An alternative version of the OSPREY software is consistent with the computational experiments described in our 2015 RECOMB paper:

      Jou JD, Jain S, Georgiev I, Donald BR. BWM*: A novel, provable ensemble- based dynamic programming algorithm for sparse approximations of computational protein design. Proceedings of the 19th Annual International Conference on Research in Computational Molecular (RECOMB), Warsaw, Poland, 2015.(In Press)
    That version of OSPREY can be downloaded here. There are several changes in the code for this version to incorporate the BWM* algorithm, and is based on a prior version of OSPREY. An additional README documenting changes is available here.

    For general redesign problems, you are probably better using the most recent version of the standard OSPREY distribution, since this version has improved user interface and functionality.

  6. A version of OSPREY consistent with the experiments in:

      Reeve SM, Gainza P, Frey KM, Georgiev I, Donald BR, Anderson AC. Protein design algorithms predict viable resistance to an experimental antifolate. Proc Natl Acad Sci U S A. 2015 112 (3), 749-754
    can be found here. This version is based on OSPREY 1.0 and requires mpi to run. Since this study, we have significantly enhanced the capabilities of OSPREY with not only improved modeling of backbone flexibility, but also efficient multi-state design, fast sparse approximations, partitioned rotamers for more accurate energy bounds, and a computationally efficient representation of molecular-mechanics and quantum-mechanical energy functions. Therefore, for general redesign problems, you are probably better using the most recent version of the standard OSPREY distribution , since this version has improved user interface and functionality.

  7. A version of OSPREY consistent with the experiments in:

      Traoré S, Roberts KE, Allouche D, Donald BR, André I, Schiex T, and Barbe S. Fast search algorithms for Computational Protein Design. Jour. Comp. Chemistry Accepted, 2015, In Press.
    can be found here. This version of OSPREY incorporates all major Cost Function Networks (CFN) algorithms and heuristics into the OSPREY package.

  8. A verison of OSPREY consistent with the experiments in:

      Jou JD, Jain S, Georgiev I, Donald BR. BWM*: A novel, provable ensemble- based dynamic programming algorithm for sparse approximations of computational protein design. J Comput Biol, 23(6):413-424, 2016.
    can be downloaded here. There are several changes in the code for this version to incorporate the BWM* algorithm, and is based on a prior version of OSPREY. An additional README documenting changes is available here.

    For general redesign problems, you are probably better using the most recent version of the standard OSPREY distribution, since this version has improved user interface and functionality.

  9. A verison of OSPREY consistent with the experiments in:

      Jain S, Jou JD, Georgiev I, Donald BR. A Critical Analysis of Computational Protein Design with Sparse Residue Interaction Graphs. PLoS Comput. Biol. 2017 (In Press)
    can be downloaded here. There are several changes in the code for this version to incorporate the Sparse A* algorithm, and is based on a prior version of OSPREY. An additional README documenting changes is available here.

    For general redesign problems, you are probably better using the most recent version of the standard OSPREY distribution, since this version has improved user interface and functionality.