Protein Docking

Here is an example of the steps used for running ZDOCK. In short, the testcase 1CGI is marked with mark_sur, some residues of the ligand are blocked, then after ZDOCK is run the top 10 predictions are produced.

• cp /home/rong/bin/uniCHARMM .
• cp /home/rong/targets/1CGI_r.pdb .
• cp /home/rong/targets/1CGI_l.pdb .
• /home/rong/bin/mark_sur 1CGI_r.pdb 1CGI_r_m.pdb
• /home/rong/bin/mark_sur 1CGI_l.pdb 1CGI_l_m.pdb
• /home/rong/bin/block.pl 1CGI_l_m.pdb 1CGI_block.txt > 1CGI_l_m_bl.pdb
• /home/rong/bin/zdock -R 1CGI_r_m.pdb -L 1CGI_l_m_bl.pdb -o 1CGI.zdock.out &
• head -14 1CGI.zdock.out > 1CGI_top10.zdock.out
• mkdir predictions
• cd predictions
• cp ../1CGI_top10.zdock.out .
• cp ../1CGI_r_m.pdb .
• cp ../1CGI_l_m_bl.pdb .
• cp /home/rong/bin/create_lig .
• /home/rong/bin/create.pl 1CGI_top10.zdock.out

For information about the contents of the ZDOCK output file and fields marked by mark_sur, please see this page. Also, here are some lectures regarding ZDOCK:

• lecture 1
• lecture 2