Directed DOCK method

While genome-wide proteomics studies provide an increasing list of interacting proteins, only a small fraction of the potential complexes are amenable to direct experimental analysis. Thus, it is important to utihze protein-protein docking methods that can ejq)lain the details of specific interactions at the atomic level. Fmthermore,... 

Recent advances in measuring the kinetics of the various electron-transfer steps in this system have been achieved by use of flash photolysis of ruthenated derivatives of cytochrome c (Ru-Cc) (17-19). In these studies [Ru(bpy)3]2+ is covalently bound to a surface residue at a site that does not interfere with the docking of cytochrome c to cytochrome c oxidase. Solutions are then prepared containing both Ru-Cc and cytochrome c oxidase, and the two proteins associate to form a 1 1 complex. Flash photolysis of the solution leads directly to the excitation of the RuII(bpy)3 site, which then reduces heme c very rapidly. This method thus provides a convenient means to observe the subsequent intracomplex electron transfer from heme c to cytochrome c oxidase and further stages in the process. 

Huang SY, Grinter SZ, Zou X (2010) Scoring functions and their evaluation methods for protein-ligand docking recent advances and future directions. Phys Chem Chem Phys 12(40) 12899-12908... 

Waldman M (2003) LigandFit a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 21 289-307. doi 10.1016/S1093-... 

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