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    "<!--NOTEBOOK_HEADER-->\n",
    "*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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    "<!--NAVIGATION-->\n",
    "< [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.00-Introduction-to-Folding.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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    "# Introduction to Folding"
   ]
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   "source": [
    "Any folding algorithm requires…\n",
    "\n",
    "\n",
    "- …a search strategy, an algorithm to generate many candidate structures (or decoys) and…\n",
    "\n",
    "\n",
    "- …a scoring function to discriminate near-native structures from all the others.\n",
    "\n",
    "\n",
    "In this workshop you will write your own Monte Carlo protein folding algorithm from scratch, and we will explore a couple of the tricks used by Simons et al. (1997, 1999) to speed up the folding search.\n",
    "\n",
    "\n",
    "## Suggested Readings\n",
    "1. K. T. Simons et al., “Assembly of Protein Structures from Fragments,” *J. Mol. Biol.*\n",
    "268, 209-225 (1997).\n",
    "2. K. T. Simons et al., “Improved recognition of protein structures,” *Proteins* 34, 82-95\n",
    "(1999).\n",
    "3. Chapter 4 (Monte Carlo methods) of M. P. Allen & D. J. Tildesley, *Computer\n",
    "Simulation of Liquids*, Oxford University Press, 1989."
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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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    "<!--NAVIGATION-->\n",
    "< [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.00-Introduction-to-Folding.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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