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Because of this the experimental structure signifies certainly a global thermodynamic minimum amount from the DNA-Zn1-Zn2 sophisticated also for that molecular simulation, thus delivering a solid assist to the dependability of your simulation protocol, and of the following success.
This is probably going A further evidence supporting the Idea which the shut SSB has not sufficient Room for equally Zn fingers, and Zn2 is the highest-affinity species to get started on the conversation, although Zn1 continues to be peripheral.
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The resulting values are approximated, nevertheless they can provide a qualitative appraisal on the binding energies linked to the protein-DNA conversation.
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the typical composition obtained as the most effective cluster with the MD simulations was then utilised given that the commencing Zn2-DNA complicated, to more dock the Zn1 monomer. An initial configuration with Zn1 docked to the SSB gap is received from HADDOCK.