Method for estimating protein-protein binding affinities

Details Method for estimating protein-protein binding affinities Method for estimating protein-protein binding affinities

2007-03-21

2010-06-15

Zhou, Shubo (Joe) (Department: 1631)

Data processing: structural design, modeling, simulation, and em

Simulating nonelectrical device or system

Biological or biochemical

Reexamination Certificate

active

07739091

ABSTRACT:
The present invention is directed to a method of predicting the binding affinity between a first molecular entity and a second molecular entity. The method includes (1) calculating the free energy of binding ΔGbindbetween the first molecular entity and the second molecular entity according to the equation (17):in-line-formulae description="In-line Formulae" end="lead"?ΔGbind=−0.82ΔX+/−+0.064ΔXc/s−0.6Xsb−0.93Xhb−0.0007Xgap−0.06ΔXtor−0.36  (17)in-line-formulae description="In-line Formulae" end="tail"?whereX+/−is the total number of exposed charged groups;Xc/sis the total number of exposed hydrophobic groups;Xsbis the total number of salt bridges;Xhbis the total number of hydrogen bonds;Xgapis the gap volume at the interface of the first molecular entity and the second molecular entity;Xtoris the total number of exposed side chain torsions;and where Δ refers to the difference between the bound and unbound states; and (2) evaluating the free energy of binding to predict the binding affinity between the first and second molecular entities.

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