OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features [article]

Mark A. Hallen, Jeffrey W. Martin, Adegoke Ojewole, Jonathan D. Jou, Anna U. Lowegard, Marcel S. Frenkel, Pablo Gainza, Hunter M. Nisonoff, Aditya Mukund, Siyu Wang, Graham T. Holt, David Zhou (+2 others)
<span title="2018-04-23">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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
more &raquo; ... 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.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/306324">doi:10.1101/306324</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cnbgcsf6mjeltmcr7yjg3q7lni">fatcat:cnbgcsf6mjeltmcr7yjg3q7lni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502135533/https://www.biorxiv.org/content/biorxiv/early/2018/04/23/306324.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b4/af/b4afc972bd91481a03da1d919c7fcc05713013d6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/306324"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>