Software:Compile Protein-DNA Interface Alignment Software

From Honiglab_public

Required executables:

1. interface_format.exe : This will format the PDB file into a new format which describes the interface in terms of the individual amino acid-nucleotide pairs and their geometric relationship. We refer to these files as *.db files.
   
   
2. interface_align.exe : This will read the 2 formatted PDB files (*.db files) and will perform the interface alignment.
   
   
3. change_nucleotide_names.pl : This will change all the DNA base names to a three letter version (e.g. T->THY). This is required for the interface_format.exe program.

Compiling executables

To compile the interface_align.exe program, go to the directory that contains all the source code, i.e. the INTERFACE_ALIGN directory from the tar file that you downloaded. Once in this directory simply type

  > gcc -o interface_align.exe *.c -lm

The same can be done for the interface_format.exe executable using the source files in the INTERFACE_FORMAT directory.

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Protein-DNA Interface Alignment Software is supported by a funding from the National Science Foundation Grant # DBI-9904841

Developed in the Honig Lab