  Proteins play crucial roles in every cellular process by interacting with
each other, with nucleic acids, metabolites, and other molecules. The resulting
assemblies can be very large and intricate and pose challenges to experimental
methods. In the current era of integrative modeling, it is often only by a
combination of various experimental techniques and computations that 3D models
of those molecular machines can be obtained. Among the various computational
approaches available, molecular docking is often the method of choice when it
comes to predicting 3D structures of complexes. Docking can generate
particularly accurate models when taking into account the available information
on the complex of interest. We review here the use of experimental and
bioinformatics data in protein-protein docking, describing recent software
developments and highlighting applications for the modeling of antibody-antigen
complexes and membrane protein complexes, and the use of evolutionary and shape
information.
