Introduction

flowchart MDockPeP server predicts protein-peptide complex structures starting with the protein structure and peptide sequence.

The prediction process consists of three steps:
(1) Modeling peptide conformers;
(2) Globally and flexibly sampling protein-peptide binding modes;
(3) Scoring and ranking the sampled binding modes.
Please go to the "About" page for the details about the MDockPeP method.

To submit a job, at least two inputs are required, the peptide sequence and the protein receptor structure. Detailed instructions about job submition and prediction results are described on the "Tutorial" page.

Job Submission

Inputs
➺  Peptide sequence :      Or upload a FASTA file:

➺  Protein structure :  

➺  Job name (optional) :  

➺   Email address (optional) :  


Advanced options (optional)▼ ➻ Peptide structure in PDB format:

➻ The number of initial peptide models to used for docking:

➻ The cutoff of bRMSD (Å) for the restriction of the peptide conformation:

➻ The exhaustiveness value for the sampling:

➻ The center of the binding site :   / /

➻ Do not show my job on the queue page

     Example: Peptide sequence : 1AWQ_pep.fasta ; Protein receptor: 1AWQ_rec.pdb

Please cite the following references for MDockPeP:
  1. Xu X, Yan C, Zou X. MDockPeP: An ab-initio protein-peptide docking server. J Comput Chem, 39: 2409-2413, 2018. [link]
  2. Yan C, Xu X, Zou X. Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction. Structure, 24: 1842-1853, 2016. [link]