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Transcript
PROTEIN STRUCTURE ANALYSIS ASSIGNMENTS Search from PubChem acetaminophen What is the IUPAC name? How many rotatable bonds there are? Which one? Visualize the structure What can you find about the carcinogenicity of the compound? Search structures from PDB for your protein How many structures do you find? What methods have been used for their determination? How do they differ? Which one do you choose and why? Is it a crystallographic or NMR structure? What is resolution? How many chains are on the structure?What is the number of amino acids in the structure? What is the number of protein atoms? What is the number and type of heteroatoms? How many secondary structural elements are there, and of what type? How are they arranged in relation to each other? Search for related structures with VAAST and Dali What did you find? Summarize the results. What conclusions can you make about the structure and protein family? Perform a sequence-based search What did you find? Summarize the results. What are the differences between results for Blast and CBlast? Explain why? Do the results differ from those for structure based search? If so, try to explain why? Classify for your protein in two ways Evaluate the quality of your protein structure Describe some problems in the protein and explain what do they mean? Analyze the structure What domains there are and what are their functions? Are there clefts of pores? What do they mean? Does the structure contain any metals? If so, which? In what reaction is the protein involved? Visualize your protein Test different visualizations and expaln for what purpose they could be used for Visualize important structural information such as catalytic and binding site and include to your report Investigate effects of variants from the LSDB - for tolerance - on protein disorder - on protein solubility - on protein stability Try to find among known disease-causing variants cases that affect these properties, test 5 to 10 variants, if necessary. You can analyze several variants in parallel.
