A Practical Guide to Cancer Systems Biology

142 A Practical Guide to Cancer Systems Biology

The smaller the full fitness is, the better the predicted binding pose.

It’s highly recommended that you download and save the result and

save them in your hard drive.

In the downloaded package, information about docking fitness is

recorded inREMARKpart of each pose of clusters.dock4.pdb.Pre-

processed structure of target protein is intarget.pdb.

To view using PyMol, you needtarget.pdbandclusters.dock4.pdb

in the downloaded package. To separate clusters.dock4.pdbinto

poses, you need to useTERas separator. In most cases, the best pose is in

the first part ofclusters.dock4.pdb, thus you can get the best pose by

copying all the text before the firstTERand paste them into a new file.

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