OSPREY 3.0: Open-source protein redesign for you, with powerful new features.


Journal Article

We present osprey 3.0, a new and greatly improved release of the osprey protein design software. Osprey 3.0 features a convenient new Python interface, which greatly improves its ease of use. It is over two orders of magnitude faster than previous versions of osprey when running the same algorithms on the same hardware. Moreover, osprey 3.0 includes several new algorithms, which introduce substantial speedups as well as improved biophysical modeling. It also includes GPU support, which provides an additional speedup of over an order of magnitude. Like previous versions of osprey, 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 entropy. Finally, we show here empirically that osprey 3.0 accurately predicts the effect of mutations on protein-protein binding. Osprey 3.0 is available at http://www.cs.duke.edu/donaldlab/osprey.php as free and open-source software. © 2018 Wiley Periodicals, Inc.

Full Text

Cited Authors

  • Hallen, MA; Martin, JW; Ojewole, A; Jou, JD; Lowegard, AU; Frenkel, MS; Gainza, P; Nisonoff, HM; Mukund, A; Wang, S; Holt, GT; Zhou, D; Dowd, E; Donald, BR

Published Date

  • November 2018

Published In

Volume / Issue

  • 39 / 30

Start / End Page

  • 2494 - 2507

PubMed ID

  • 30368845

Pubmed Central ID

  • 30368845

Electronic International Standard Serial Number (EISSN)

  • 1096-987X

International Standard Serial Number (ISSN)

  • 0192-8651

Digital Object Identifier (DOI)

  • 10.1002/jcc.25522


  • eng