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   "source": [
    "<!--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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   "metadata": {},
   "source": [
    "<!--NAVIGATION-->\n",
    "< [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Setting up a membrane protein in the bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.00-Modeling-Membrane-Proteins.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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   "source": [
    "# Modeling Membrane Proteins"
   ]
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    "## Background\n",
    "\n",
    "Membrane protiens constitute 30% of all proteins and are targets for 60% of pharmeceuticals on the market. These biomolecules are unique because their structure and function is coupled with the lipid bilayer: a self-assembling nanostructure made from hundreds of lipid types such as phospholipids and cholesterol. The goals of this workshop are to (1) learn common tasks for membrane protein modeling in PyRosetta and (2) give examples of the types of problems one can solve with this framework. \n",
    "\n",
    "<img src='Media/membranes/membrane_proteins_illustrative.png'>"
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    "id": "Dr-5ZzfcTZ8I"
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    "## Learning Objectives\n",
    "\n",
    "1.\tUse membrane tools to orient a protein in the lipid bilayer\n",
    "2.\tIdentify and visualize membrane protein pores and cavities\n",
    "3.  Apply membrane tools to obtain membrane data for modeling\n",
    "4.\tInterpret model quality using terms from franklin2019, the membrane energy function\n",
    "5.\tIllustrative example of predicting the ∆∆G of mutation within the bilayer\n",
    "6.  Illustrative example of membrane protein-protein docking\n"
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   "source": [
    "## Suggested Readings\n",
    "\n",
    "1.\tAlford RF, Leman JK et al., “An Integrated Framework Advancing Membrane Protein Modeling and Design,” PLOS Computational Biology. 2015;11(9).\n",
    "2.\tAlford RF, Fleming PJ, Fleming KG, Gray JJ (2020) “Protein structure prediction and design in a biologically-realistic implicit membrane” BioRxiv\n",
    "3.\tKoehler Leman J, Muller BK, Gray JJ (2017) “Expanding the toolkit for membrane protein modeling in Rosetta” Bioinformatics 33(5):754-756. \n",
    "4.\tKoehler Leman J & Gray JJ (2015) “Computational modeling of membrane proteins” Proteins Structure, Function, and Bioinformatics 83(1):1-24. \n"
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   "metadata": {
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   "source": [
    "## Chapter Contributors\n",
    "\n",
    "- Rebecca Alford (Johns Hopkins University)\n",
    "- Kathy Le (Johns Hopkins University)"
   ]
  },
  {
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   "execution_count": null,
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!--NAVIGATION-->\n",
    "< [RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Setting up a membrane protein in the bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.00-Modeling-Membrane-Proteins.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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