The server only requires a PDB file of the target protein and an approximate definition of the desired binding site (query region) as input. The file can be uploaded or directly downloaded from the PDB database by inserting its PDB ID. An optional email address to be informed about the job completion can be provided.
If the PDB file contains more than one chain by default all chains will be used, the user can specify specific chains by providing chain names. For example:
will tell the server to only use chains A and C from the provided PDB structure.
The structure of the target protein is displayed in the web page as soon as the file is uploaded.
The chain identifier "P" should not be used as it denotes the designed peptide in the output file.
Only atoms specified in the ATOM PDB records are considered.
The binding site (query region) can be defined in two ways:
Upon clicking the button “Check binding site in Jmol and confirm your selection”, the selected residue(s) and, if the second option is selected, the region corresponding to the binding site (query region) are highlighted (in darkcyan and darkviolet, respectively) in the input structure in the graphics window.
Once the process is started (by clicking the “Submit” button), a page containing a Job Id that can be bookmarked will be displayed:
If the user provided an email, she/he will receive a mail from email@example.com with the Job Id and another mail upon job completion.
The Job Id can be inserted in the box in the left most part of the input page to verify the status of the job and to visualize the results upon completion.
Results are kept on the server for two weeks
* The list of peptides includes the number of times each sequence has been obtained and the corresponding representative peptide. The protein peptide complexes can downloaded in PDB format (chain P denotes the peptide).