Interactive Slides Structural bioinformatics & drug discovery

Interactive Slides for Biomolecular Visualization

1.Take a photo of physical model of the four helix bundle cytochrome b562, PDBID: 256b, with your name written underneath.

2.(a) How many hemoglobin structures that cause sickle cell anemia (hemoglobin S) are deposited in the PDB?   (b)What is the part of the protein (buried/surface) that this amino acid mutation occurs? (c) Discuss why normal hemoglobin (Glu 7, Asp73) is less likely to form fibers than Hemoglobin C-Harlem (D73N, Chain B + E7V, Chain H).

3.(a)How many CDK kinases with resolution < 1.5Å are deposited in the PDB? (b)Send me a picture of the CDK-ligand interaction from 4FKL.

4.Learn to make a poster of the structure from Nishimasu H, et al.’s CRISPR-Cas9 paper (Source: http://www.sciencedirect.com/science/article/pii/S0092867414001561)

5. Create a GIF animation of a protein you choose.

 

Please email the link to homework to duangrudee.tan@mahidol.ac.th

Directory YourID_YourFirstName/

1)YourName_practical.pdf

2)YourName_physicalmodel.jpg

3)YourName_CRISPR.png

4)YourName_Protein.gif

5)YourName_YourDrug.pptx

Next week

From knowledge you learn today + MANORAA.org, please pick one drug from (478,G39, STI, TOP, UNK) and make a presentation of the drug, its target protein, pathways, human organ, expression levels and, if available, SNPs. Explain how the amount of hydrogen bonds + ionic interaction and structural conservation might be useful for drug design.

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