Protein docking problem

Given the multitude of approaches now used to dock small molecules and peptides to proteins, why should the protein-protein docking problem require its own approaches Could one make do with the software packages developed for these related problems Unfortunately, the answer is usually no. 

Lenhof, H. P. (1997). New contact measures for the protein docking problem. In RECOMB97 - Proceedings of the first annual international conference on computational molecular biology. ACM. 

Wang, H. (1991). Grid-search molecular accessible surface algorithm for solving the protein docking problem./. Comp. Chem. 12, 746-750. 

In the sequel, we first outline the basics of the deterministic global optimization approach, aBB, which has been used extensively to study the protein structure prediction, dynamics of protein-protein folding, and protein docking problems. This is followed by a comprehensive study of ab initio modeling for structure prediction of single-chain polypeptides in Section III. An... 

H. Wang,/. Comput. Chem., 12,746-750 (1991). Grid-Search Molecular Accessible Surface Algorithm for Solving the Protein Docking Problem. 

Throughout this chapter, we roughly separate docking approaches by their treatment of protein flexibility. Within the two broad categories (rigid body and flexible docking), the docking problem can be separated into two subproblems ... 

Refinement of Protein Interfaces Incorporating Solvation Application to the Docking Problem. 

Jackson RM, Gabb HA, Sternberg MJE (1998) Rapid refinement of protein interfaces incorporating solvation Application to die docking problem. J. Mol. Biol. 276(1) 265—285... 

The GA approach has also been applied to the docking problem with dihydrofolatereduc-tase, arabinose binding protein, and sialidase... 

This section is dedicated to the scoring aspect of the docking problem. Various approaches are discussed that try to capture the essential elements of protein-ligand interactions in computationally efficient scoring functions. The discussion focuses on general approaches rather than individual functions. The reader is referred to Table 7.2 for original references to the most important scoring functions. 

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