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Abstract
Three-dimensional structures of only a small fraction of known protein-protein complexes
are currently known. Meanwhile, computational methods are of increasing importance
to provide structural models for known protein-protein interactions. Current protein-protein
docking methods are often successful if experimentally determined partner proteins
undergo little conformational changes upon binding. However, the realistic and computationally
efficient treatment of conformational changes especially of the protein backbone during
docking remains a challenge. New promising approaches of flexible refinement, ensemble
docking and explicit inclusion of flexibility during the entire docking process have
been developed. A significant fraction of known protein-protein interactions can be
modeled based on homology to known protein-protein complexes which in many cases also
requires efficient flexible refinement to provide accurate structural models.