OSPREY 3.0：开源蛋白质设计软件，拥有强大的新功能。
OSPREY 3.0: Open-source protein redesign for you, with powerful new features.
机构信息
Department of Computer Science, Duke University, Durham, North Carolina, 27708.
Toyota Technological Institute at Chicago, Chicago, Illinois, 60637.
出版信息
J Comput Chem. 2018 Nov 15;39(30):2494-2507. doi: 10.1002/jcc.25522. Epub 2018 Oct 14.
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. © 2018 Wiley Periodicals, Inc.
摘要
我们呈现了 osprey 3.0，这是 osprey 蛋白质设计软件的一个全新且极大改进的版本。Osprey 3.0 具有一个方便的新 Python 接口，极大地提高了它的易用性。与在相同硬件上运行相同算法的 osprey 的以前版本相比，它的速度快了两个数量级以上。此外，Osprey 3.0 包括几个新算法，这些算法引入了实质性的加速以及改进的生物物理建模。它还包括 GPU 支持，这提供了超过一个数量级的额外加速。与 osprey 的以前版本一样，Osprey 3.0 提供了一系列独特的优势，包括可证明的设计算法，这些算法在设计和模型构象熵期间考虑了连续的灵活性。最后，我们在这里通过经验证明 osprey 3.0 可以准确预测突变对蛋白质-蛋白质结合的影响。Osprey 3.0 可在 http://www.cs.duke.edu/donaldlab/osprey.php 免费获得，并作为开源软件使用。©2018 威利期刊公司
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