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  {
   "source": [
    "# Predicted ligand binding sites in interaction interface\n",
    "\n",
    "If you have a protein of interest and want to know the predicted ligand binding sites of it which are also in a protein-protein interaction, you can first make use of the annotations API for a UniProt accession to get all annotations from PDBe-KB partners for the protein.\n",
    "\n",
    "The predicted ligand site annotations are provided by `p2rank` and `3dligandsite`. Post process this response to filter the `accession` field for these providers. This gives all UniProt residues which are annotated as a predicted ligand binding site. \n",
    "\n",
    "\n"
   ],
   "cell_type": "markdown",
   "metadata": {}
  },
  {
   "source": [
    "\n",
    "![alt](../images/web4_annotations.png)"
   ],
   "cell_type": "markdown",
   "metadata": {}
  },
  {
   "source": [
    "## 1) Get the annotations data for UniProt accession `P61626`"
   ],
   "cell_type": "markdown",
   "metadata": {}
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import requests\n",
    "from pprint import pprint\n",
    "\n",
    "accession = \"P61626\"\n",
    "annotations_url = f\"https://www.ebi.ac.uk/pdbe/graph-api/uniprot/annotations/{accession}\"\n",
    "\n",
    "annotations_data = requests.get(annotations_url).json()\n",
    "\n"
   ]
  },
  {
   "source": [
    "## 2) Filter the data for providers `p2rank` and `3dligandsite`"
   ],
   "cell_type": "markdown",
   "metadata": {}
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "all_ligand_binding_residues = list()\n",
    "\n",
    "for provider_data in annotations_data[accession][\"data\"]:\n",
    "    if provider_data[\"accession\"] in [\"p2rank\", \"3dligandsite\"]:\n",
    "        residues = [x[\"startIndex\"] for x in provider_data[\"residues\"]]\n",
    "        all_ligand_binding_residues.extend(residues)\n"
   ]
  },
  {
   "source": [
    "## 3) Get interacting residues for the UniProt accession\n",
    "\n",
    "Use the interface residues for a UniProt accession API call to get this data.\n",
    "\n",
    "![interface residues](../images/web4_interface_residues.png)\n"
   ],
   "cell_type": "markdown",
   "metadata": {}
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "interface_url = f\"https://www.ebi.ac.uk/pdbe/graph-api/uniprot/interface_residues/{accession}\"\n",
    "\n",
    "interface_data = requests.get(interface_url).json()\n"
   ]
  },
  {
   "source": [
    "## 4) Filter `interface_data` on common residues\n",
    "\n"
   ],
   "cell_type": "markdown",
   "metadata": {}
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "all_interface_residues = list()\n",
    "\n",
    "for item in interface_data[accession][\"data\"]:\n",
    "    interacting_residues = [x[\"startIndex\"] for x in item[\"residues\"] if x[\"startIndex\"] in all_ligand_binding_residues]\n",
    "    all_interface_residues.extend(interacting_residues)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "output_type": "stream",
     "name": "stdout",
     "text": "Residues of P61626 which is predicted ligand binding site and part of protein-protein interaction are [53, 64, 67, 71, 76, 78, 82, 122, 126, 128, 40, 42, 45, 96, 115, 53, 62, 96]\n"
    }
   ],
   "source": [
    "print(f\"Residues of {accession} which is predicted ligand binding site and part of protein-protein interaction are {all_interface_residues}\")"
   ]
  }
 ]
}