Workshop Description

The overall goal of this workshop is to introduce learners to the kinds of information available about macromolecular structure and how to generate a homology model based on a known structure. The 3 day course will cover; how to access structural data from databases to find a template structure, how to manipulate the data using rosetta and how to view and validate the results using pymol with the end goal being to assess how changes from the template can affect function.

Day 1

  • Introduction to structure/function relationship
  • Finding a known structure in the PDB using target sequence
  • Explanation of the PDB entry, what different kinds of information can be extracted? Online visualisation tools
  • Downloading PDB file and exploring its contents using command line
  • Different techniques for structure determination and validation metrics
  • Setting up directories for day 2

Day 2

  • Opening up Python and loading the PyRosetta toolbox
  • Preparing sequence files and PDB files for Comparative modelling
  • Modification in PyRosetta, basic PyRosetta commands
  • Generating multiple homology models potentially using different start points
  • Understanding Rosetta’s scoring system and selecting the best model

Day 3

  • Visualization using Pymol
  • Different ways to load files into Pymol
  • Different ways to represent structure in Pymol
  • Focusing into and highlighting particular residues
  • Comparison and alignment to known structure(s)
  • Exporting images and movies

Technical Requirements

We have 10 iMac computers with the relevant software installed. If you prefer to bring your own laptop, please installed the following prior to the start of class:

Python (2.7 or 3)
Windows – https://www.python.org/downloads/windows/

Pymol
Mac – https://pymolwiki.org/index.php/MAC_Install (look at the open source installation)
Windows – https://pymolwiki.org/index.php/Windows_Install
Linux – https://pymolwiki.org/index.php/Linux_Install

PyRosetta
Mac (precompiled) – http://www.pyrosetta.org/dow
Windows – http://www.pyrosetta.org/documentation/windows

Feel free to come see me in Boyer 529 if you need help installing anything.

Instructor

Dr. Marcus Gallagher-Jones is a postdoctoral fellow working in the Rodriguez lab at UCLA. He received his BS in Biochemsitry from Durham University and his PhD in Biophysics from University of Liverpool before working for 2 years in the department of Physics at UCLA. His main interests are in structural analysis across many length-scales (atomic to whole cell) using electron and x-ray diffraction. His expertise include: structural biology, algorithm design, digital image processing, phase retrieval and tomographic reconstruction.

Email: marcusgj@chem.ucla.edu

Workshop Details

Prerequisites: None*
Length: 3 days, 2hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28
*Unix & Basic Python are recommended

Fall Dates

Oct. 24 – 26, 1 – 3pm