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 4-35. 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. If a PDB entry and chain IDs (e.g., 1aqw:A) are provided, the protein structure will be automatically downloaded from Protein Data Bank. Allowed sizes of the protein are 31-1000 amino acids. 1.3 Peptide sequence only MDockPeP2 can be used to generate conformatinal ensembles for a peptide. For this purpose, please provide a peptide sequence only and do not provide a protein structure. 1.4 An example of the inputs (PDB: 1AWQ): Peptide sequence (FASTA file): 1AWQ_pep.fasta Protein receptor structure: 1AWQ_rec.pdb
2.1 The number of initial peptide models to be used for docking According to our systematic studies on the PepPro dataset, the recommended value is 200 (default). Note: The computing cost is in proportion to the number of peptide conformers used for docking. 2.2 Blocking residues from the binding site The user is allowed to upload a list of protein residues which will be blocked during the docking process. An example of the list for blocking residues: blocking_residues.txt
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.
