Tutorial

1. Required inputs
2. Advanced options
3. Job status
4. Results

1. Required inputs

1.1 Peptide sequence
The peptide sequence can be provided either by entering single-letter amino acid codes or by uploading a FASTA file. The sequence length of the peptide should be within 4-20.

1.2 Protein receptor structure
The server recognizes only the PDB format for the protein receptor structure. Although the uploaded protein file will be cleaned (e.g. deletion of the solvates and ligands) after submittion, uploading a pre-checked structure is recommended. Allowed sizes of the protein are 31-1000 amino acids.

1.3 An example of the inputs (PDB: 1AWQ):
Peptide sequence (FASTA file): 1AWQ_pep.fasta
Protein receptor structure: 1AWQ_rec.pdb


2. Advanced options (optional)

2.1 Peptide structure
The server allows users to upload a peptide structure as one of the initial peptide structures for docking. The sequence in the uploaded peptide structure should to be identical to the previously provided peptide sequence.

2.2 The number of initial peptide models to be used for docking
According to our systematic studies on the peptiDB database, the recommended value is 3 (default).

Note: If this value is set to 1 and a peptide structure is provided, only the user-provided peptide structure will be used as the initial peptide structure for docking.

2.3 The cutoff of bRMSD (Å) for the restriction of the peptide conformation
The cutoff vaule of bRMSD is used to restrict the peptide conformation during the sampling. If bRMSD was larger than the cutoff (default = 5.5 Å), the peptide conformation was restored to the initial peptide conformation and rigid-flexible sampling was repeated. See the reference [1-2] for details.

2.4 The exhaustiveness value for the sampling
The value of exhaustiveness is set for a docking with each peptide conformer. The default value is 100, namely each docking calculation contains 100 independent runs.

2.5 The searching box
Users are allowed to define a binding location by providing the XYZ coordinates of the center of the searching box. The users are recommended to provide the size of the box. Otherwise, the box size will be automatically determined by the peptide length: (3.8 × peptide_sequence_length + 40) Å.

  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]


3. Job status

After a job is submitted, the MDockPeP server will immediately examine the uploaded files. A pop-up page will inform the user whether the job is successfully submitted. If not, the ERROR information will be reported on this page.
Once the job is successfully submitted, the job status is monitored on the "Queue" page. When the job is waiting for computational resource allocation, the job status is "Pending". Once the job starts to run, the status will be changed to "Running". The user will receive an email (if provided) notification after the job is completed. Then, the status will be changed to "Done" or "Error".

Note: If the user selects the option "Do not show my job on the queue page" on the submission page, the job status will not appear on the "Queue" page. In this case, the only way to know the status is through email notification.


4. Results

4.1 How to receive the results
When the job is completed, a result page will be created. There are three ways to obtain the link of the result page:
a) The link is provided on the pop-up page after the job is successfully submitted.
b) The link will be sent to the user by email when the job is completed.
c) The user can find the job on the "Queue" page through keyword search, and then click the corresponding "Job ID".

4.2 The result page
On the result page, top 10 and top 500 predicted peptide binding modes are available for download.
The top 10 models are also displayed on the result page via a JavaScript library 3Dmol.js. The user can click the "View" button to display the individiual models. A PDB file for each peptide binding mode can be downloaded through the "Download" link.

4.3 Display and analyze results on your local machines
A number of molecular visualization programs are available to display the predicted protein-peptide binding modes. Here, we use ViewDock option in Chimera as an example:
a) Download the protein receptor structure "rec_clean.pdb" and the predicted peptide binding modes "Top10_pep_models.pdb" or "Top500_pep_models.pdb";
b) Open Chimera and click "Menu: File ... open" to open the receptor pdb file ("rec_clean.pdb");
c) Click "Menu: Tools ... Surface/Binding Analysis ... ViewDock" to open ViewDock and load the predicted peptide binding modes (e.g. "Top10_pep_models.pdb"). Once the file is successfully loaded, the program will ask for the file type. Choose "Dock 4, 5 or 6".