Warning

This page is located in archive.
Go to the latest version of this course pages.
Go the latest version of this page.

Make sure you can answer the following questions:

- Describe the levels of protein structure.
- Explain in general the idea of the “Branch and Bound” method.
- Explain the meaning of the words when used for genes: analog, homolog, paralog, ortholog and xenolog.
- What is a protein ligand?

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`

- Go to https://blast.ncbi.nlm.nih.gov/Blast.cgi and click “Protein blast”.
- Enter the sequence and enter “Homo sapiens (taxid:9606)” as organism.
- Click the blast button and wait. This may take up to several minutes.
- Look for the best matching protein. It should be: “monoamine oxidase A”
- Enter this protein name to UniProt.
- Check whether the result has a secondary sequence annotation and find the position respective to the BLAST match.

Use the above-described procedure to learn most about the following peptide sequence: `TEYAINKLRQLYVLRC`

.

A hint: the sequence is a part of a frequent protein domain.

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:

i | j | k |
---|---|---|

g1(i,2) = 5 | g1(j,8) = 9 | g1(k,13) = 3 |

g1(i,3) = 2 | g1(j,9) = 7 | g1(k,14) = 4 |

g1(i,4) = 8 | g1(j,10) = 6 | g1(k,15) = 1 |

i/j | j/k | i/k |
---|---|---|

g2(i,j,2,8) = 1 | g2(j,k,8,13) = 7 | g2(i,k,2,13) = 1 |

g2(i,j,2,9) = 2 | g2(j,k,8,14) = 8 | g2(i,k,2,14) = 2 |

g2(i,j,2,10) = 2 | g2(j,k,8,15) = 7 | g2(i,k,2,15) = 5 |

g2(i,j,3,8) = 5 | g2(j,k,9,13) = 1 | g2(i,k,3,13) = 5 |

g2(i,j,3,9) = 6 | g2(j,k,9,14) = 6 | g2(i,k,3,14) = 6 |

g2(i,j,3,10) = 4 | g2(j,k,9,15) = 8 | g2(i,k,3,15) = 4 |

g2(i,j,4,8) = 7 | g2(j,k,10,13) = 11 | g2(i,k,4,13) = 1 |

g2(i,j,4,9) = 3 | g2(j,k,10,14) = 12 | g2(i,k,4,14) = 2 |

g2(i,j,4,10) = 4 | g2(j,k,10,15) = 13 | g2(i,k,4,15) = 4 |

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

courses/bin/tutorials/tutorial11.txt · Last modified: 2022/06/03 14:34 by klema