Beginning Docking Tutorial
- After signing up for an account and logging into the server, you will be presented with the screen below
- The first thing you will want to do is choose a job name. If you don't choose a name for your job, it will default to the job id.
- In each docking job, you will have a receptor and ligand. We will walk through choosing the receptor. You have two options for
choosing a receptor. You can choose a structure present in the PDB or upload your own PDB by clicking on Upload PDB.
- You can optionally choose what chains to use in docking by specifying them below where the pdb file was chosen. The chains should be
single letters and white-space separated. If no chains are specified, all chains in the file will be used.
- As an example input, we will consider the first case in the the Protein-Protein Docking Benchmark 3.
Our receptor will be chain A of 1QQU and ligand will be Chain B of 1BA7. Since 1QQU's only chain is chain A, we do not need to specify the chain.
- We will then be taken to view the queue. We can track the progress of our job from there along with any jobs ahead of yours.
- Depending on the queue on the supercomputer and the size of your protein, docking will usually complete within a few hours. You will be notified via
e-mail when your job completes. You can then find your job in your results.
- Clicking on the id of your job will bring you to the results for that job. Here, you can view and download the results of your docking. If you have
extra information on the nature of your complex, you can view the results for coefficient sets favoring electrostatics or hydrophobicity. Clicking
on the number above a picture will download that model as a pdb file for your viewing. You can also download all the displayed models or all models
for all coefficients.
- By default, the server only displays the top 10 models. You can change the number of models displayed if you don't find a satisfactory complex among
the top 10.
- To analyze these results, we download the first model and view it in Pymol. The receptor is named model.000.00_0001
and the ligand is named model.000.00_0002. We have also downloaded the pdb for 1avx and aligned it to the receptor since it remains stationary
during docking. We can see that our ligand (in blue) accurately predicts where the trypsin inhibitor in 1avx binds trypsin.
If you have any questions, please look to see if it is addressed on the help page. If you have any suggestions, please