1. OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features
- Author
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Jeffrey W. Martin, Bruce R. Donald, Elizabeth Dowd, Marcel S. Frenkel, Aditya Mukund, Pablo Gainza, Siyu Wang, Hunter M. Nisonoff, Anna U. Lowegard, Graham T. Holt, Mark A. Hallen, David Zhou, Adegoke Ojewole, and Jonathan D. Jou
- Subjects
0303 health sciences ,Speedup ,business.industry ,Computer science ,Protein design ,Parallel computing ,010501 environmental sciences ,Python (programming language) ,01 natural sciences ,03 medical and health sciences ,Software ,Open source ,Software design ,business ,computer ,030304 developmental biology ,0105 earth and related environmental sciences ,computer.programming_language - Abstract
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.
- Published
- 2018
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