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 the job submission.

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: 200 50 100 500 1000

➻ 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