Summer Drug Design Course 2010

Programs Tutorials Course Files Docking Results


Most of the techniques dicussed in class will be available to you through the web. However there are a few programs that are unavailable online and must be installed.
Molecular Viewer
Discovery Studio Visualizer
Chemical Drawing
Symyx Draw


  1. Go to and enter your PDB ID in the search bar.
  2. Follow the "Download Files" link on the upper right and select "PDB File (Text)", save this somewhere convenient.
  3. Using Notepad or your favorite text editor create two new files, named protein.pdb and ligand.pdb
  4. Open the PDB file you downloaded with the text editor and highlight, copy, and paste the protein atoms into the protein.pdb file you just created. Highlight, copy, and paste the ligand atoms into the ligand.pdb file as well.
    NOTE(1)If you have Cl, or Z atoms these can be ignored.
    NOTE(2)If you have a multimeric structure you should determine which chain and ligand you need first by visual examination while at
  5. Go to and highlight, copy and paste the contents of the ligand.pdb file you created in step 4 into the text box just under "Paste your input here (PDB coordinates, MDL MOLfile, text drawing). See below for instructions."
  6. Select "Chirality Yes", "Full charges Yes", "Energy minimization No" and then "Run PRODRG".
  7. Scroll down to "Docking / MD simulations" and click on the "AUTODOCK PDBQ file version 3.0 link".
  8. Highlight the contents in the text box and copy them to a new text file. Call this ligand.pdbq
  9. Go to MEDock
  10. Under "Ligand" select "PDBQ" and "PRODRG".
  11. Erase the "Paste the AUTODOCK 3.0 PDBQ file output here" text in the ligand box.
  12. Under Protein, select "PDB" and "Copy & Paste".
  13. Copy and paste the contents of the ligand.pdbq file into the Ligand text box. Copy and paste the contents of the protein.pdb file into the Protein text box.
  14. Click on "proceed" at the bottom right.
  15. Accept the defaults including leaving "random seed" empty by clicking on "proceed"
  16. Write down your "Task ID" and enter your email address. This is the address where you will receive your results.

Course Files

Lecture Materials
Week 1
Week 2
Week 3
Supplemental Docking Files

Autodock Modified Ligand
Docking Results
Docking Results
1c9a1 6a903 8ef4d 9a0dd 716db be280
e3318 37191 f348c d6561 7e877 59456
5abbe 2fada f359b 35b74 7e8d8 4de3f
cb3a5 d1040