{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# An overview of Biobox" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Welcome! In this notebook we will overview Biobox's main features, and point to relevant publications where they were used. Biobox is developed by the Degiacomi group (www.degiacomi.org) in Durham University (UK), and is downloadable from Github, https://github.com/Degiacomi-Lab/biobox. Its API is available here: https://Degiacomi-Lab.github.io/biobox/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This overview covers the following topics:\n", "\n", "* [Selecting atoms from a (multi)PDB](#select)\n", "* [Protein conformations clustering](#cluster)\n", "* [Protein polyhedral assemblies](#polyhedra)\n", "* [Super-coarse grain modelling](#supercg)\n", "* [Density map cutoff via Collision Cross Section](#density)\n", "* [Calculating cross-linking distances](#xlink)\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "