21 Mart 2010 Pazar

Graph of Day 11: Protein bound tree

Recently, I attend Chemical Engineering course which is related to bioinformatics and computational biology. It is closer to chemical engineering perspective but also professor tends to integrate our perspective which is almost zero knowledge about some topics :). Protein is formed by amino acids, and each protein is the product of sequence on the genome.

I obtain one protein from PDB, and using matlab, I visualize the protein( 2WTT: P73 Tumor Protein). Interestingly it is a tree structure with atoms and bounds( Figure on the right above ).

Then, when we form complex structure in the form of several proteins. This time we obtain graphs that is formed with several trees. I don't know do people work on it, but analyzing the graphs would be an alternative to sequence matching algorithms. Maybe in the near future, I will have better understanding on these topics.

Same protein with apha helixes;

And just amino acids with different colors;

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