Protein-Protein Docking Methods

Abstract

A critical review of published methodology used in docking proteins and of current understanding of the problems associated with the inherent flexibility of proteins is presented. The underlying assumption made in the past of docking two rigid bodies (six degrees of freedom) is clearly not applicable to most protein-protein interactions as induced fit is the rule rather than the exception. Nevertheless, significant progress is being made as investigators increase flexibility of the docking partners with the availability of increased computational power. In the extreme case, however, docking of two proteins is equivalent to predicting the structure of the complex from the two sequences alone.