Definition
Predict the final atomic resolution structure of a protein–protein complex starting from the coordinates of the unbound conformation of each component protein.
Discussion
Introduction
Most successful approaches to protein–protein docking use multistage hierarchical methods typically consisting of an initial global rigid body search (or a simplified reduced search based on known information) to identify a number of candidate protein–protein complexes followed by a more sophisticated refinement procedure. After searching, filtering, and refining, the predicted complexes are rescored based on a sophisticated scoring function for selecting the lowest energy complex. The native protein–protein complex is at the global free energy minimum; therefore those models with the lowest (free) energy should be the most similar to the native complex.
Approaches to Conformational Searching
Exhaustive Rigid Body Searching
The first step in docking two known protein structures is to generate...
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Armen, R.S., May, E.R., Taufer, M. (2011). Protein Docking. In: Padua, D. (eds) Encyclopedia of Parallel Computing. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-09766-4_452
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DOI: https://doi.org/10.1007/978-0-387-09766-4_452
Publisher Name: Springer, Boston, MA
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