Software:Protein-DNA Interface Alignment Software Tutorial

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Quick tutorial: How to align two protein-DNA interfaces from PDB files

Here we demonstrate how to perform an alignment between the two homoeodomain-DNA complexes 1hdd.pdb (Engrailed) and 9ant.pdb (Antp).

1. Determine the complex you want to align. If the PDB files that you have contain multiple chains, then you might want to break them up into individual pdb files. For example, if the PDB file contained two protein chains,A and B, and two DNA chains, C and D. Then you may want to break up the PDB file FOO.pdb into a FOO_A.pdb and a FOO_B.pdb which contain the protein chains A and B, respectively, and both DNA chains. The reason for this is that if you are aligning two PDB files that both contain 2 protein chains, the algorithm maintains the order of the chains as they appear in the PDB file and simply assumes that they belong to one big chain. Therefore, if a PDB file FOO_1.pdb contained protein chains A and B, in that order, and FOO_2.pdb contained protein chains F and G, in that order, then the algorithm could not align A to G and B to F simultaneously. However, for this example I will leave the multi-chain PDB files of 1hdd and 9ant unaltered.
   
   
2. Change base (nucleotide) names from one letter to three letter version, e.g. T->THY. To do this simply run
   
    > perl    change_nucleotide_names.pl   1hdd.pdb -- this will re-write 1hdd.pdb with the 3 letter names
   
   
3. Format the two PDB files:
   
    > interface_format.exe    -i 1hdd.pdb  &nbsp >    1hdd.db
    > interface_format.exe    -i 9ant.pdb  &nbsp >    9ant.db
   
   
4. Align 1hdd.db and 9ant.db:
   
    > interface_align.exe    -i 1hdd.db    -j 9ant.db   > output
   
   Output should look like:
   
   

   1hdd.pdb  9ant.pdb     S(i,j)  <br> 
   LYS D 57  LYS B  57     =    5.9 
   LYS D 55  LYS B  55     =    3.5
   	:
   	:	
   ARG C  5  ARG A   5     =    2.7  
   
   57 aligned residues IAS = 318.0 

   
   

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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