Multiscale Protein and Peptide Docking
The number of functional protein complexes in a cell is larger by an order of magnitude than the number of proteins. The experimentally determined three-dimensional structures exist for only a very small fraction of these complexes. Thus, the methods for theoretical prediction of structures of protein assemblies are extremely important for molecular biology. Association of two (or more proteins) always induces conformational changes of the individual components. In many cases, these induced changes are relatively small and involve mostly the side chains at the association interface. In such cases, the approaches of rigid-body docking of two (or more) structures are quite successful. Quite frequently, however, the docking-induced conformational changes are significant. In such cases, prediction of the resulting structures is extremely challenging. The cases, where experimental structures of some components do not exist, are yet even more difficult. In this chapter, we briefly overview the existing in silico docking methods and describe a multiscale strategy of unrestricted flexible docking of proteins and peptides.
KeywordsDocking Simulation Residual Dipolar Coupling Interface Residue Protein Docking Docking Procedure
- Ołdziej S, Czaplewski C, Liwo A, Chinchio M, Nanias M, Vila JA, Khalili M, Arnautova YA, Jagielska A, Makowski M, Schafroth HD, Kaźmierkiewicz R, Ripoll DR, Pillardy J, Saunders JA, Kang YK, Gibson KD, Scheraga HA (2005) Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci USA 102:7547–7552PubMedCrossRefGoogle Scholar