1.1 Ligand structure
Please upload a ligand structure in the following formats: smi; mol; mol2; or sdf;
An online server for chemical format conversion: OpenBabel

1.2 Protein receptor
Please upload a protein sequece ([50,1000] residues) in FASTA format or using PDB code and chain id.

1.3 Examples of inputs
   a) Ligand structure : lig.smi; lig.mol; lig.mol2; or lig.sdf;
   b) Protein sequence: protein.fasta; or using PDB code and chain id: 3KMX:A

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 (up to) 5 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.

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