Protein-docking algorithm

The first step in the development of a protein docking algorithm is to examine the known complexes to establish the principles of molecular recognition. Following earlier work [10], there are reviews that examined the interactions between hetero-protein complexes [4, 7]. These analyses have focussed on the static structure of the complexes. A major problem in protein docking is to cope with the conformational flexibility that occurs on complex formation. Accordingly, we have analyzed the conformational changes on complex formation for 39 pairs of structures of proteins in... 

Chen R, Li L, Weng Z (2003) ZDOCK an initial-stage protein-docking algorithm. Proteins... 

This approach has also been used to measure the amount of surface area buried in molecular complexes. The buried surface area is equal to the sum of the surface areas of each monomer minus the surface area of the complex computed as if it were a single molecule. Protein docking algorithms often rank their predicted complexes by the size of the interface, as measured by buried surface area. 

GOLD Automated ligand-protein docking program with genetic algorithm and force field-based scoring function... 

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