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Tutorial 4

Updated for 2022W semester and on. This tutorial takes at least two one-hour dry lab sessions. In 2023W semester, each dry lab session is 1.5 hours.

Resources

This section includes links to websites that are useful for protein analysis that can be used in the final project.

Seconary Structure Prediction

Disordered Prediction

3D Structure Prediction: Homology modelling and Threading

AlphaFold

Structure alignment

PDB related

Practices

DSSP

Calculation of secondary structure using dssp.

  1. update the content in a Ubuntu terminal: cd ~/bioc4010; git pull
  2. enter the tut4 folder: cd tut4
  3. run dssp 1UBQ.pdb to calculate SS of the ubiquitin structure (PDB code: 1UBQ)
  4. if you want to download and calculate another structure, use a script under tut4 named getpdb.sh. To use the script, make sure it is executable by typing ls -l in the tut4 folder and check whether it has a permission of -rwxr--r--. If there is no "x" (meaning executable) in the permission, type chmod u+x getpdb.sh first to make it executable. Then when in the tut4 folder, run ./getpdb.sh 2r2o will download the strucuture cooridnate for pdb item 2R2O, and the FASTA format file from RCSB. After downloading the pdb file, you can run dssp 2R2O.pdb to calculate the secondary structures of 2R2O.

PyMOL

You can get an educational version from PyMOL.org and install it on your own laptop for Molecular Graphics. For this tutorial, the PyMOL has already been installed in the Virtual Machine. First download and read the Molecular Graphics using PyMOL instructions and undertstand the background and the tasks. You have to save the PyMOL instruction file by clicking right-button and save it. And open it using Microsoft Word. Or if you clicked the link, then you should click the "view raw" in the openned page to save the file for viewing in Microsoft Word.

  • Launch of the program: type pymol in the terminal.
  • Get familiar with the PyMOL interface and knows how to manipulate a molecule.
  • Follow the instructions in the above document and finish all the tasks.
  • Try run dss command in PyMOL when a structure is loaded and shown in cartoon mode.
  • Finish assignment #12 posted on BrightSpace.

AlphaFold: Assignment #13

  • Read and follow the instructions of the Jupyter Notebook version of AlphaFold2 on Google Colab
  • Predict the structure of the sequence in the fish.9x.ubl.fa file, which is the putative ubiquitin-like domain of zebrafish Usp9X protein.
  • Calculate the sequence identity of the putative UBL domain of the zebrafish Usp9x with human Usp9x
  • Choose the structure ranked number #1, compare with predicted structure with that of PDB 5VBD, align the two structures in PyMOL, describe any difference you see and explain why a high sequence identity does not yield an identical structure.

Hint: When you download the structure of PDB 5VBD, download from the RCSB database and choose the Biological Assembly 2 from the database, which contains two copies of the molecules. The experimentally determined structure is a domain-swapped dimer in the solution.

Todo

  • Convert the PyMOL guide into markdown format
  • Add instructions for using PyMOL to store a session, and different scenes, exporting figures.