student-notebooks/05.00-Structure-Refinement.ipynb

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    "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);\n",
    "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*"
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    "< [Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.00-Structure-Refinement.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
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    "# Structure Refinement"
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    "One of the most basic operations in protein structure and design algorithms is manipulation of the protein conformation. In Rosetta, these manipulations are organized into movers. A `Mover` object simply changes the conformation of a given pose. It can be simple, like a single φ or ψ angle change, or complex, like an entire refinement protocol.\n",
    "\n",
    "## Suggested Reading\n",
    "- P. Bradley, K. M. S. Misura & D. Baker, “Toward high-resolution de novo structure prediction for small proteins,” Science 309, 1868-1871 (2005), including Supplementary Material.\n",
    "- Z. Li & H. A. Scheraga, “Monte Carlo-minimization approach to the multiple-minima problem in protein folding,” Proc. Natl. Acad. Sci. USA 84, 6611-6615 (1987).\n",
    "\n",
    "## PyRosetta Workshop 5 Link\n",
    "https://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshop5_StructureRefinement.pdf\n",
    "\n",
    "## Appendix A Link\n",
    "https://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshops_Appendix_A.pdf"
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    "**Chapter contributors:**\n",
    "\n",
    "- Kathy Le (Johns Hopkins University); this chapter was adapted from the [PyRosetta book](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8) (J. J. Gray, S. Chaudhury, S. Lyskov, J. Labonte)."
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