The program SSBOND takes a coordinate file in PDB format and lists all pairs of amino acids that could form a disulfide bond if the two residues where cysteines. The main reasons to engineer disulfide bonds is to stabilize the protein or protein complex or to study protein function, e.g. the role of structural flexibility.
SSBOND first calculates the distance of C-beta atoms of pairs of residues. When this distance is small enough to form a potential disulphide bond, the program will attempt to build the disulfide bond by molecular modeling. For all plausible disulfide bond conformations the program will cary out a local energy minimization to yield an optimized structure. However, this minimization does not include non-bonded interactions with neighbouring protein atoms. The final result is a list of residue pairs that could form a disulfide bond if mutated to cysteines. For each pair multiple conformations may be listed and for each of these the energy is given. The lower the energy the less strain is introduced by the engineered disulphide. The program can also write out a new PDB file with the modeled disulfide bond to allow visual inspection by the user. Documentation on how to use the program is included at the top of the source code. However, the easiest way to run the program is by using the Online form.
SSBOND is written in standard FORTRAN77 and has been compiled on a wide variety of hardware platforms (but not Windows/Macintosh). Please contact the author if you encounter problems while compiling the source code.Click on the links while pressing the shift key to download the files
If you use the results of the program SSBOND in publications then you can use the following reference:
Hazes, B. & Dijkstra, B.W. (1988). Model building of disulfide bonds in proteins with known three-dimensional structure. Protein Engineering 2: 119-125