AutoPLI is a fullly automated server for predicting protein-ligand interactions. For more details about the server and methods, please go to the "About" page or read the references (at the bottom of this page).

To submit a job, two inputs are required:
(1) A ligand structure;
(2) A protein sequence.

Detailed instructions about job submition and prediction results are described on the "Tutorial" page.

Job Submission
Inputs
➺   Upload a ligand structure (accepted formats: smi, mol, mol2, or sdf):  

➺  Copy and paste the protein sequence ([50,1000] residues in FASTA format):
     
     Or upload the sequence from your local computer:
     Or provide PDB code and chain id:

➺  Job name (optional):  

➺   Email address (optional)
? Optional but recommended.
If provided, you will receive an email notification after your job is completed.
:   

➺ Do not show my job on the queue page
   Example: Ligand structure : lig.smi; lig.mol; lig.mol2; or lig.sdf;
                     Protein receptor: protein.fasta; or using PDB code and chain id: 3KMX:A
References:
  1. Xu X, Zou X. AutoPLI: A Fully Automated Server for Predicting Protein-ligand Interactions. (Preparing)
  2. Xu X, Ma Z, Duan R, Zou X. Predicting protein-ligand binding modes for CELPP and GC3: workflows and insight. Journal of Computer-Aided Molecular Design, 33: 367-374, 2019. [link]
  3. Duan R, Xu X, Zou X. Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor. Journal of Computer-Aided Molecular Design,32: 103-111, 2018. [link]
  4. Xu X, Yan C, Zou X. Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015. Journal of Computer-Aided Molecular Design, 31: 689-699, 2017. [link]