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
? The peptide length shold be within 4-15
:      Or upload a FASTA file:

➺  Protein structure
? PDB format.
The number of residues should be within 31-1000
:  

➺  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

Advanced options (optional)▼ ➻ The number of initial peptide models to be used for docking:

➻ Peptide structure in PDB format:

➻ The cutoff of bRMSD (Å) for the restriction of the peptide conformation:
? The input value should be [1.0, 8.0]. The default is 5.5.
Å

➻ The exhaustiveness value for the sampling:
? The input vaule shoud be [50, 200]. The default is 100.


➻ The center of the searching box
? Please also provide the size of the box. Otherwise it will be determined by the peptide length.
:   / /

      The size of the searching box:
? A cubic box. Default value = (3.8 × peptide_sequence_length + 40) Å.
Å


     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]