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Make sure you can answer the following questions:
A simple, although not always reliable, way to discover the secondary structure of a peptide sequence is to look up a protein with similar primary sequence in a database. Let us try this! The task is to obtain the secondary structure of the following peptide sequence: HYLCKYVINAIPPTLTAKIHFRPELPAERNQLIQRLA
HYLCKYVINAIPPTLTAKIHFRPELPAERNQLIQRLA
Recall the branch-and-bound threading algorithm from the lecture.
Suppose we have three segments (i, j, k), each of which includes three amino acids. For a given sequence there are three possible starting positions for each segment. (i ∈ {2,3,4}, j ∈ {8,9,10}, k ∈ {13,14,15}) We will be using the simple lower bound:
Suppose that you are given the following values for the scores of the individual segments and the scores for segment interactions:
Using this information, compute the optimal threading.
The purpose of this tutorial is to put our hands on a software for comparative protein structure modelling, namely the MODELLER. We will go through a basic tutorial for this software. At the end this tutorial, you should have a better understanding of what such software is capable of.
Download the MODELLER version for your operating system from: https://salilab.org/modeller/download_installation.html (Note: It is also available from official repositories of some GNU/Linux distributions.)
You need to register yourself in order to obtain a license here: https://salilab.org/modeller/registration.html You should provide your university e-mail in the registration form.
We will follow this tutorial from the MODELLER webpages: https://salilab.org/modeller/tutorial/basic.html.
For those who are interested to learn more about MODELLER, there are also advanced tutorials: https://salilab.org/modeller/tutorial/
If you are interested, you may also have a look at the I-TASSER software.
A tutorial on homology modelling from the university of Frankfurt.
Branch and bound threading example taken from https://www.biostat.wisc.edu/bmi776/spring-17/lectures/threading.pdf threading.pdf