1.1 Ligand structure
A ligand structure should be provided by a MOL2 file (Click Here for the MOL2 format).
An online server for chemical format conversion: OpenBabel

1.2 Protein receptor
The protein receptor can be provided by either an UniProt access number/id or 3D structure (less than 1000 residues) in PDB format:
   a) If an UniProt access number/id was provided, the prediction would be based on available PDB structures of the protein (Click Here for the details)
    b) If a PDB structure was provided, the ligand would docked to the PDB structure. In this case, the user was recommended to provide the binding site location through coordinates of the binding site center. If the binding site information was not provided, a global docking would be performed.

1.3 An example of the inputs (PDB: 1AWQ):
   a) Ligand structure (MOL2 file): lig.mol2
   b) Protein receptor: UniProt access number Q96RI1 (UniProt id NR1H4_HUMAN)
       or   3D structure in PDB file: rec.pdb (Binding site location: 43.2/14.3/2.7)

After a job is submitted, the AutoPLI server will immediately examine the uploaded files. A pop-up page will inform the user whether the job is successfully submitted. If not, the ERROR information will be reported on this page.

Once the job is successfully submitted, the job status is monitored on the "Queue" page. When the job is waiting for computational resource allocation, the job status is "Pending". Once the job starts to run, the status will be changed to "Running". The user will receive an email (if provided) notification after the job is completed. Then, the status will be changed to "Done" or "Error".

Note: If the user selects the option "Do not show my job on the queue page" on the submission page, the job status will not appear on the "Queue" page. In this case, the only way to know the status is through email notification.

3.1 How to receive the results
When the job is completed, a result page will be created. There are three ways to obtain the link of the result page:
a) The link is provided on the pop-up page after the job is successfully submitted.
b) The link will be sent to the user by email when the job is completed.
c) The user can find the job on the "Queue" page through keyword search, and then click the corresponding "Job ID".

3.2 The result page
On the result page, top 10 predicted ligand binding modes are available for download.
The top 10 models are also displayed on the result page via a JavaScript library 3Dmol.js. The user can click the "View" button to display the individiual models. A PDB file for each binding mode can be downloaded through the "Download" link.

If similar co-bound ligands (SHAFTS HybridScore >= 1.2) against the query ligand were found, corresponding PDBs and SHAFTS scores would be reported.

3.3 Display and analyze results on your local machines
The following are a few molecular visualization programs can be used to display and analyze protein-ligand interactions based on complex PDB structures:
UCSF Chimera
SMALL-MOLECULE DRUG DISCOVERY SUITE