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OSPREY 3.0: Open‐source protein redesign for you, with powerful new features
Author(s) -
Hallen Mark A.,
Martin Jeffrey W.,
Ojewole Adegoke,
Jou Jonathan D.,
Lowegard Anna U.,
Frenkel Marcel S.,
Gainza Pablo,
Nisonoff Hunter M.,
Mukund Aditya,
Wang Siyu,
Holt Graham T.,
Zhou David,
Dowd Elizabeth,
Donald Bruce R.
Publication year - 2018
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25522
Subject(s) - python (programming language) , speedup , computer science , software , open source , open source software , software package , r package , computational science , parallel computing , programming language
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.