I have done Protein-Protein docking in ZDOCK server. After getting results of Top 5 prediction, how can I get binding energy or docking score to conclude results?
The docking score is in the output file (text file) produced by zdock. It's the last column starting from row 6; the first five rows are headers. You can read the description/formatiing of the zdock output file here: http://zlab.umassmed.edu/zdock/zdock_output_file.shtml and an example is given here: http://zdock.umassmed.edu/results/example_zdock_2B42/job49836.zd3.0.2.out
Zdock uses a rather simplistic scoring function, so there is no bindng energy and it can't be directly derived from the zdock score. Read more about zdock scoring function in the original paper: http://onlinelibrary.wiley.com/doi/10.1002/prot.10389/full . To get the estimates of binding energy you'd have to take the docked poses from zdock and run MD simulations.
Dear All,
How to do analysis on Pydock Result? and I can't see the Autodock vina result in Ligplot. Can anybody help me in this regs? Thanks in Advance....
For Pydock analysis I hope the following paper will help DOI: 10.1002/prot.21419. To visualize 2D conformation of Autodock Vina you may use Discovery Studio software.
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