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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",
    "< [Docking](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.00-Protein-Docking.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.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": [
    "# Fast Fourier Transform Based Docking via ZDOCK\n",
    "Keywords: FFT, ZDOCK"
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    "There are several servers available based on fast Fourier transforms (FFTs). These servers are able to quickly carryout a global, grid-based matching searches.\n",
    "\n",
    "\n",
    "Go to the ZDOCK server (http://zdock.bu.edu) and upload trypsin (2PTN) and its inhibitor (1BA7 chain B) for docking. __Do this in groups in order to not overload the server.__ When the jobs have finished (typically under an hour), download the output file. You will have to also download a script for creating complexes from the output file. Use the script to generate the top five models. \n",
    "    \n",
    "__Question:__ Are these models similar or diverse? How so? Are any of the models similar to the crystal structure of the bound complex (1AVW)?\n",
    "    \n",
    "(Other servers include SmoothDock (http://structure.pitt.edu/servers/smoothdock), ClusPro (http://cluspro.bu.edu),, Haddock (http://haddock.chem.uu.nl), and GRAMM-X (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx). Any of these provide global docking services to create models that might be useful for refinement by RosettaDock.)"
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    "<!--NAVIGATION-->\n",
    "< [Docking](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.00-Protein-Docking.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.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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