Executables

I.    To score a PDB file, and to get the profile scores and neighbor residues of each residue, use GetProfile.
      Details are given in the Readme file.
      Here is a sample profile output file for 2ACY.

      Download the appropriate executable as a binary file. The Readme file
      should also be saved into the same directory where the executable file is saved.
      The default command would look like

 > GetProfile ../pdbs/1ERX.pdb A ../pdbs/profiles/profile_1ERX 

• To run in Linux, use GetProfile_linux (compiled using g++ 3.2.2 in Linux 9).
• To run in Sun, use GetProfile_sun (compiled using g++ 3.3 in SunOS 5.9).
• To run in IRIX, use GetProfile_irix (compiled using g++ 3.3 in IRIX64).

II.   To do virtual mutagenesis - get the total scores of the native and the mutated structures,
      as well as the profile scores of both, use Mutate.
      Any number of residues (up to all residues) could be mutated in one go.
       Here is a sample mutated profile output file for 2CI2, when the following mutations were done -
       25 ARG 32 TRP 50 MET 61 MET

      Again, download the appropriate executable as a binary file. The Readme file
      should also be saved into the same directory where the executable file is saved.
      Default command looks identical to that for GetProfile. The program
      Mutate would ask the user to input the number of residues to be mutated.
      If a non-zero number is given, the user is prompted to enter the residue numbers of the
      residues to be mutated and the three-letter identities of the residues to which each of them
      are to be changed in succession. For example,   85 LEU 132 TRP 50 ALA 2 ARG .

      The native score (before mutation) and the difference in total
      score (mutated - native) are reported. Profile scores of each residue in the native as well as
      mutated structures are written to file (when the filename is given in the command line).

• To run in Linux, use Mutate_linux (compiled using g++ 3.2.2 in Linux 9).
• To run in Sun, use Mutate_sun (compiled using g++ 3.3 in SunOS 5.9).
• To run in IRIX, use Mutate_irix (compiled using g++ 3.3 in IRIX64).