RT Journal Article
SR Electronic
T1 OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 306324
DO 10.1101/306324
A1 Mark A. Hallen
A1 Jeffrey W. Martin
A1 Adegoke Ojewole
A1 Jonathan D. Jou
A1 Anna U. Lowegard
A1 Marcel S. Frenkel
A1 Pablo Gainza
A1 Hunter M. Nisonoff
A1 Aditya Mukund
A1 Siyu Wang
A1 Graham T. Holt
A1 David Zhou
A1 Elizabeth Dowd
A1 Bruce R. Donald
YR 2018
UL http://biorxiv.org/content/early/2018/04/23/306324.abstract
AB 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.We present the third major release of the OSPREY protein design software, along with comparisons to experimental data that confirm its ability to optimize protein mutants for desired functions. osprey 3.0 has significant efficiency, ease-of-use, and algorithmic improvements over previous versions, including GPU acceleration and a new Python interface.