Time: Fri, July 9, 9:00 am - noon
Place: Biotech Park I (medical campus) Suite 212
Organizers: Glen Kellogg and Jason Rife
Audience: Primarily 1st year

Topics

1. Forcefields: building and optimizing in 3-D
   • Cyclohexane: boats and chairs
   • Local and global minima
   • More organic molecules, including a few recreational pharmaceuticals
2. Visualization tricks
   • lines, sticks, balls and spacefill models
   • surface rendering
3. Beating the local minima problem
   • Systematic search
   • Molecular dynamics

Resources of session

• Reading: General molecular modeling. Peter J. Steinbach, NIH.
  [Heavy going. Read it if it does you any good]
• Reading: Hydrophobicity: is LogPo/w more than the sum of its parts? Kellogg GE, Abraham DJ (2000).
  Eur J Med Chem 35:651-661.
  [Glen's seminar regarding HINT in writing]

Before coming to the session

• Please review Glen's seminar by going through the Eur J Med Chem article
• Please look at the Peter Steinbach's online tutorial. If it makes sense to you, pursue it. Otherwise don't worry.
• Please review where you're going tomorrow and how to get there. If you don't know, ask Austin, Nathan, or any 2nd year student..
  
  
  

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