{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Simulating Glycan Shielding\n", "\n", "Proteins that are glycosylated have parts of their surface covered by the attached glycan chains. This makes them inaccessible for certain interactions such as with antibodies. To ascertain the \"shielding effect\" of glycans on a protein surface one can use molecular dynamics to obtain high quality conformers, albeit at a high computational cost. \n", "\n", "Glycosylator offers a simple quick-simulation tool to sample glycan conformations on a glycosylated scaffold without the need for extensive computational resources. To that end Glycosylator provides the `GlycoShield` class and the top-level `quickshield` function. These will generate a dataframe containing an \"exposure score\" for each residue in the scaffold, which is a measure of how much a residue is \"covered\" by glycan chains and thus not exposed to the environment. Lower values indicate higher coverage by glycans and vice versa." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import glycosylator as gl\n", "gl.visual.set_backend(\"py3dmol\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Using `quickshield`\n", "\n", "The most convenient way to simulate shielding is the `quickshield` function. It accepts a glycosylated `Scaffold` object as input and returns a `GlycoShield` which contains the data we are interested in. Let's see how:" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "application/3dmoljs_load.v0": "
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n",
" jupyter labextension install jupyterlab_3dmol
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n",
" jupyter labextension install jupyterlab_3dmol
| \n", " | chain | \n", "resname | \n", "serial | \n", "exposure | \n", "
|---|---|---|---|---|
| 0 | \n", "A | \n", "LEU | \n", "401 | \n", "249.983373 | \n", "
| 1 | \n", "A | \n", "GLU | \n", "34 | \n", "333.743532 | \n", "
| 2 | \n", "A | \n", "ARG | \n", "153 | \n", "134.149625 | \n", "
| 3 | \n", "A | \n", "ALA | \n", "278 | \n", "167.025529 | \n", "
| 4 | \n", "B | \n", "LEU | \n", "495 | \n", "177.947479 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 573 | \n", "A | \n", "ILE | \n", "400 | \n", "270.514356 | \n", "
| 574 | \n", "A | \n", "TYR | \n", "152 | \n", "80.195666 | \n", "
| 575 | \n", "A | \n", "TYR | \n", "277 | \n", "208.773678 | \n", "
| 576 | \n", "A | \n", "THR | \n", "33 | \n", "324.323760 | \n", "
| 577 | \n", "B | \n", "VAL | \n", "494 | \n", "241.743316 | \n", "
578 rows × 4 columns
\n", "