Assignment 4

Assignment 4.1
  • Run through the tutorial in the Introduction to JMOL from Wiley. Answer the two questions at the end, and provide screenshots of your answers.
  • Create a 3D MOL/SD file for Octane. You might find open babel useful! .Save this file
  • Download JMOL
  • Run the jmol.jar file and open the file for Octane
  • Create a van-der-waal's surface (you'll need to right-click for the menu)
  • Export a JPEG image of the file (File->Export)
  • Measure the distance from the first to the last carbon in Angstrom. You will need to double click to start and finish the measurement. Note you will need to change the default distance measurement units.
  • Report in your answer the JPEG image of Octane and your measurement.

Assignment 4.2

  • Go to PubChem (http://pubchem.ncbi.nlm.nih.gov/) and find five compounds that are kinase inhibitors (you can search for “kinase inhibitor”) and five that are not (any kind of search you like)
  • Paste the SMILES for your 10 structures in turn into the Molinspiration bioactivity calculator (http://www.molinspiration.com/cgi-bin/properties) and note the predicted Kinase values
  • Plot the values on the curves on ALL the graphs at http://www.molinspiration.com/docu/miscreen/druglikeness.html - you can plot the points on the image of the graphs, using two different colors for real kinase inhibitors and non-inhibitors
  • Write a short paragraph describing whether you think the Kinase predictions are good, based on your analysis of the plots on the Kinase and other graphs
  • Submit: a list of your 5 inhibitor and 5 non-inhibitor SMILES; graphs with your 10 compounds plotted on for all four graphs; and your short discussion