Assignment 1. Protein structure analysis.

1) (20 points) Select four proteins with known structures which belong to the same family and have pairwise sequence identity of no more than 70%. The length of each protein should be less than 180 residues and structure resolution better than 1.8Å.

2) (20 points) Construct a hydrophobicity profile and a secondary structure propensity profile for all four proteins. For one of the proteins compare profile values with residue positions in the protein and their secondary structures.

3) (20 points) Build a multiple sequence alignment and all possible pairwise structure alignments for these proteins. Plot the values of structure similarity against sequence similarity for all pairs. Evaluate and discuss correlation between sequence and structure similarity.

4) (20 points) Locate one fragment of high sequence similarity and one fragment of low sequence similarity in the alignment form (2). Investigate correlations between structure and sequence similarity for these fragments. Describe a possible role of the secondary structure content in these correlations.

5) (20 points) Identify functionally important site(s) in four proteins. Describe their biological role and their relationship to the structure conservation.

The report should be submitted by email as a Word or PDF file with the filename "b731_25_hw1_Your_Name.doc or .pdf". The string "b731_25_hw1_Your_Name" should be also included in the message subject line.

Due by 11:59 pm on October 23, 2025 October 26, 2025.

Late submissions are subject to penalty, 10 points per day.  

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