SSBOND

SSBOND predicts sites where disulphibe bonds can be introduced into proteins of known structure. Given a Protein Data Bank (PDB) file, the program will return a list of residue pairs that, if mutated to cysteines, will form proper disulphide bonds. The dihedral angles describing the disulphide bond and an estimate of the energetic strain introduced are given for each modeled disulphide bond. Low values for the energetic strain suggest a more ideal conformation, however, this is just an estimate and it does not include steric interactions with the remainder of the protein. It is therefore strongly recommended that the modeled disulphide bonds are visually inspected. To this end, the program produces an output PDB file with the modeled disulphide bonds. For PDB files with multiple chains it is best to upload a single chain at a time, unless interchain disulphide bonds are desired.

For residues that can participate in more than one disulphide bond, the last modeled side chain conformation will be given. If this is not the desired conformation, then rerun the form with a file containing just the two amino acids between which a disulphide bond should be modeled. Alternatively, you can install the program locally to get more flexibility on modeling. To get a copy of the standalone Fortran 77 program click here.

To use this server, use the Browse button below to locate the PDB file on your harddisk. Clicking Upload will submit your request and return the results. All uploaded files are deleted immediately after analysis and will be treated confidentially.




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