Assignment 1. Protein structure analysis.

Find four structurally similar proteins (Z-score > 3) with pairwise sequence similarity of less than 70%. At least one of these proteins should be a human protein. 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. Discuss and evaluate correlation between sequence and structure similarity. Locate fragments of high and low sequence similarity in these proteins. Investigate correlations between structure and sequence similarity for several such fragments. Describe a possible role of the secondary structure content in these correlations. Identify functionally important site(s) in these proteins and their relationship to the structure conservation. Write a report (2-4 pages). The report should be submitted by email as a Word or PDF file with the filename "b731_07_hw1_Your_Name.doc or .pdf". The string "b731_07_hw1" should be also included in the message subject line.

Due October 30, 2007.

Assignment 2. Protein modeling.

Select a protein sequence from one of the sequence databases that has a homolog in PDB with at least 30%, but not more than 70% of sequence identity. (Recommended length of the selected sequence is 120-300 residues). Predict the three-dimensional structure for the selected sequence using at least two methods (e.g., one of the fold recognition algorithms and homology modeling with SwissModel). Analyze the quality of your model using one of the structure validation or verification tools. Evaluate separately one of the biologically important parts of the structure (e.g., an active site or binding site). Present the results of the modeling with description of all the steps in HTML format with interactive molecular visualization tools and post the files on the Internet. Submit the URL by email with the string "b731_07_hw2" in the message subject line.

Due November 27, 2007.