- Docking Simulation 141
Materials
- Ligand file (containing only single compound)
- Protein target structure file
Procedure
I. In your browser, navigate to http://www.swissdock.ch/, or search for
“SwissDock” in your search engine.
II. You’re in “Home” tab right now. Please switch to “Submit Docking”
tab (Fig. 6(a)).
III. After switching to “Submit Docking” tab, fill the fields in target
selection, ligand selection, and description panels (Fig. 6(b)).
You may submit your file by clicking on “upload file (max 5 MB)”. You
may also submit by PDB ID (target) or ZINC ID (ligand), etc. if you
already know the ID or name of the protein target or ligand (Figs. 6(c)–
6(d)).
After you see “Successful setup” text appear right after you submit
your target or ligand, you can click on “inspect” on the right of “Suc-
cessful setup” to review your model before running docking simulation.
It is highly recommended that you review your model before doing the
computation.
It is highly recommended that you fill your e-mail such that you will
receive a notification after the job is finished.You can assign binding site (if you have such information) and set
docking operation type after clicking on “Show extra parameters” above
“Start docking” button.
IV. It takes about 30 minutes to finish a docking run.
If you did not receive any notification about your docking, you may have
a typo in your email address and should try again later. If such condition
persists, please contact maintenance team by using “contact” tab.
V. You may view the result online if your computer system has java sup-
port, or you may view the result using UCSD chimera by following the
instructions in the result page, or you may download the result into your
hard disk and view them with your favorite molecular viewer (Fig. 6(e)).
The result poses are grouped into clusters, and the clusters are sorted
by average full fitness. In general, element 0 of cluster 0 has the best
full fitness.