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Protein design
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====Scoring binding predictions==== Protein design energy functions must be adapted to score binding predictions because binding involves a trade-off between the lowest-[[Thermodynamic free energy|energy]] conformations of the free proteins (<var>E<sub>P</sub></var> and <var>E<sub>L</sub></var>) and the lowest-energy conformation of the bound complex (<var>E<sub>PL</sub></var>): : <math>\Delta_G = E_{PL} - E_P - E_L </math>. The K* algorithm approximates the binding constant of the algorithm by including conformational entropy into the free energy calculation. The K* algorithm considers only the lowest-energy conformations of the free and bound complexes (denoted by the sets <var>P</var>, <var>L</var>, and <var>PL</var>) to approximate the partition functions of each complex:<ref name=donald10 /> : <math>K^* = \frac{\sum\limits_{x\in PL} e^{-E(x)/RT}}{\sum\limits_{x\in P} e^{-E(x)/RT}\sum\limits_{x\in L} e^{-E(x)/RT}}</math>
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