CRYSTAL STRUCTURE Kd SERVER        PDB to free energy

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HOW IT WORKS

Your PDB file should contain muliple chains (proteins), and preferably no water or ligands.
You need to specify which chains should be dissociated from the complex.

Example 1:
PDB file contains chains A, B and C. You need to calculate Kd for equilibrium:
ABC = AC+B
Chains to dissociate=A,C (B is stationary, A,C are mobile)
// you can also use Chains to dissociate=B (A,C is stationary, B is mobile) with the same result
Example 2:
PDB contains crystal symmetry mates. Chains usually have the same names, for example, A,B; A,B; A,B; A,B
Your tasks prior to using the server are (1) to give chains unique names, such as A,B,C,D,E,F,G,H
and (2) prepare separate PDB files for each interface you want to study: A,B,C,D (pdb1), C,D,E,F (pdb2) etc.
Chains to dissociate: pdb1: A,B;  pdb2: C,D etc. 


 

 
   
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  Chain(s) to dissociate from the PDB*
         For example: PDB has chains A,B   You enter: A
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