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

Hallen, M. A.; Martin, J. W.; Ojewole, A.; Jou, J. D.; Lowegard, A. U.; Frenkel, M. S.; Gainza, P.; Nisonoff, H. M.; Mukund, A.; Wang, S.; Holt, G. T.; Zhou, D.; Dowd, E.; Donald, B. R.

doi:10.1101/306324

bioRxiv · 10.1101/306324

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

Hallen, M. A.·Martin, J. W.·Ojewole, A.·Jou, J. D.·Lowegard, A. U.·Frenkel, M. S.·Gainza, P.·Nisonoff, H. M.·Mukund, A.·Wang, S.·Holt, G. T.·Zhou, D.·Dowd, E.·Donald, B. R.

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Abstract

We present O_SCPCAPOSPREYC_SCPCAP 3.0, a new and greatly improved release of the O_SCPLOWOSPREYC_SCPLOW protein design software. O_SCPLOWOSPREYC_SCPLOW 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 O_SCPLOWOSPREYC_SCPLOW when running the same algorithms on the same hardware. Moreover, O_SCPLOWOSPREYC_SCPLOW 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 O_SCPLOWOSPREYC_SCPLOWO_SCPCAP, C_SCPCAPO_SCPLOWOSPREYC_SCPLOW 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 O_SCPLOWOSPREYC_SCPLOW 3.0 accurately predicts the effect of mutations on protein-protein binding. O_SCPLOWOSPREYC_SCPLOW 3.0 is available at http://www.cs.duke.edu/donaldlab/osprey.php as free and open-source software.\n\nO_TEXTBOX\n\nWe 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.\n\nC_TEXTBOX\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC=\"FIGDIR/small/306324v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (54K):\norg.highwire.dtl.DTLVardef@f08b0dorg.highwire.dtl.DTLVardef@393b61org.highwire.dtl.DTLVardef@16997ddorg.highwire.dtl.DTLVardef@1713405_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Hallen, M. A., Martin, J. W., Ojewole, A., Jou, J. D., Lowegard, A. U., Frenkel, M. S., Gainza, P., Nisonoff, H. M., Mukund, A., Wang, S., Holt, G. T., Zhou, D., Dowd, E., Donald, B. R.. 2018-04-23. OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Features. https://doi.org/10.1101/306324

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