How to submit a new job
Take the CCR5 chemokine receptor (PDB code: 4MBS) as an example.
- The protein chains will be rendered as lines.
- The ligands will be rendered as sticks.
- The ions and waters will be rendered as dots.
- The protein surface will be constructed asynchronously.
The WebGL canvas supports the following keyings:
- Default: rotate
- Ctrl: translate
- Shift: zoom in/out
- Ctrl + shift: slab
Adjust the center and the size so that the search space covers your desired binding site just right.
Fill in your email to receive notification upon job completion. Fill in any anonymous email should you not want to receive notification.
Filter compounds according to your application. Avoid choosing too many compounds to make sure your job can be completed within a reasonable time. Current docking speed is 1 second per ligand.
Submit your job. Only protein chains and ions will be sent to the server. Ligands and waters will be discarded.
Check your job status in the topmost table.
In some cases we do not want to send all protein chains to the server. Take the influenza A virus nucleoprotein (PDB code: 2IQH) as an example. It is a trimer and contains three chains. The binding site of a chain is occupied by the tail loop of a neighboring chain. Therefore use a text editor to manually remove two chains in advance, and repeat the above procedure.
How to enable WebGL to visualize the target protein
Check the compatibility table for support of WebGL in desktop and mobile browsers at http://caniuse.com/webgl.
IE11 has experimental support of WebGL.
Chrome 32 enables WebGL by default.
Firefox WebGL can be enabled by following these instructions.
Safari WebGL can be enabled by following these instructions.
How to get rid of "must conform to PDB specification"
If your protein is not downloaded from the official PDB website but obtained from homology modeling or other software, it is likely that the tooltip must conform to PDB specification will show up when you click the submit button. It is due to the fact that many software programs output PDB files that are somewhat customized and do not strictly following the official PDB specification. Here is a checklist for your PDB file:
- Each line must consist of exactly 80 columns, including
CONECT lines. For example, if your
TER line consists of only 3 characters, you must append 77 extra spaces to align it to 80 characters wide.
TER line must be present at the end of a series of
ATOM lines to specify the end of a chain.
ATOM line should incorporate the atom type at columns 77 to 78. Although this is not a necessity, without it our parser will fail to recognize the atom type and you will end up with discrete white dots in the canvas. The good news is that, in most cases, it will not affect the subsequent docking results.
How to use the REST API to programmatically submit multiple jobs in batch and query for job status
Submit a new job via HTTP POST
curl http://istar.cse.cuhk.edu.hk/idock/jobs -d '&description=4MBS&email=Jacky@cuhk.edu.hk¢er_x=150¢er_y=109¢er_z=22&size_x=18&size_y=17&size_z=15&mwt_lb=390&mwt_ub=420&lgp_lb=1&lgp_ub=3&nrb_lb=4&nrb_ub=6&hbd_lb=2&hbd_ub=4&hba_lb=4&hba_ub=6&chg_lb=0&chg_ub=0&ads_lb=0&ads_ub=10&pds_lb=-40&pds_ub=0&psa_lb=60&psa_ub=80&receptor=ATOM 1 N PRO A 19 148.930 114.148 5.178 1.00138.31 N
ATOM 2 CA PRO A 19 149.869 115.263 5.360 1.00138.99 C
ATOM 3 C PRO A 19 151.021 115.224 4.348 1.00144.31 C
ATOM 4 O PRO A 19 150.914 114.542 3.320 1.00144.78 O
ATOM 5 CB PRO A 19 150.357 115.076 6.800 1.00138.04 C
ATOM 6 CG PRO A 19 149.222 114.376 7.496 1.00140.40 C
ATOM 7 CD PRO A 19 148.354 113.704 6.460 1.00137.06 C
TER 2743 GLN A 313
Obtain existing jobs via HTTP GET
Count the number of compounds satisfying your custom filtering conditions via HTTP GET
curl http://istar.cse.cuhk.edu.hk/idock/ligands -Gd 'mwt_lb=400&mwt_ub=500&lgp_lb=0&lgp_ub=5&nrb_lb=2&nrb_ub=8&hbd_lb=2&hbd_ub=5&hba_lb=2&hba_ub=10&chg_lb=0&chg_ub=0&ads_lb=0&ads_ub=12&pds_lb=-50&pds_ub=0&psa_lb=20&psa_ub=100'