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DDG and interaction score problem

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DDG and interaction score problem

Dear All,

I have designed some protein binders based on pre-structured models.

In Rosetta, ddg for designed protein binders are about -20 r.e.u. The problem is that when I assessed them with some servers like PRODIGY ( predicting the binding affinity in protein-protein complexes, unbelievably the ΔG (kcal mol-1) for designed proteins are competently more than pre-structured models. For example, ΔG for designed protein and pre-structured model are -7.6 kcal mol-1 and -12.6 kcal mol-1 respectively. As far as I know, the more negative  Gibbs free energy (ΔG) results in the formation of stronger complexes.

I do not understand what is the problem.

Post Situation: 
Mon, 2018-04-09 22:54