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.

中文翻译：

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OSPREY 3.0：为您重新设计开源蛋白质，具有强大的新功能

我们推出了 osprey 3.0，这是 osprey 蛋白质设计软件的一个经过重大改进的新版本。Osprey 3.0采用了方便的新Python界面，大大提高了其易用性。在相同硬件上运行相同算法时，它比以前版本的 osprey 快两个数量级以上。此外，osprey 3.0 还包含多种新算法，这些算法显着提高了速度并改进了生物物理建模。它还包括 GPU 支持，可提供超过一个数量级的额外加速。与 osprey 的早期版本一样，osprey 3.0 提供了优于其他设计软件的独特优势，包括可证明设计算法，可在设计和模型构象熵过程中实现持续灵活性。最后，我们凭经验证明 osprey 3.0 准确预测了突变对蛋白质-蛋白质结合的影响。Osprey 3.0 作为免费开源软件可从 http://www.cs.duke.edu/donaldlab/osprey.php 获取。© 2018 Wiley 期刊公司。