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MDockPeP2 is an online server predicting protein-peptide complex structures starting with a peptide sequence and a protein structure. Details >>

Required inputs:
★ A peptide sequence and a protein structure: predicting protein-peptide complex structures.
☆ A peptide sequence only: generating an ensemble of peptide bound conformations.

Click Here for more details about submitting the job.

Job Submission
Inputs
➺  Peptide sequence
? The peptide length shold be within 4-35
:  
? e.g., HAGPIA

      Or upload a FASTA file:

➺  Protein structure
? PDB format.
The number of residues should be within 31-1000
:  or       provide "PDB:ChainIDs":  
? e.g., 1awq:A


➺  Job name :                 

➺   Email address
? 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 peptide conformers to be used for docking:

➻ Blocking residues from the binding site (Details):


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

Please cite the following reference for MDockPeP2:
  1. Xu X, Zou X. Predicting Protein-peptide complex structures by accounting for peptide flexibility and physicochemical environment. J. Chem. Inf. Model. 2022, 62: 27-39. DOI: https://doi.org/10.1021/acs.jcim.1c00836