  Protein-peptide interactions play essential functional roles in living
organisms and their structural characterization is a hot subject of current
experimental and theoretical research. Computational modeling of the structure
of protein-peptide interactions is usually divided into two stages: prediction
of the binding site at a protein receptor surface, and then docking (and
modeling) the peptide structure into the known binding site. This paper
presents a comprehensive CABS-dock method for the simultaneous search of
binding sites and flexible protein-peptide docking, available as a users
friendly web server. We present example CABS-dock results obtained in the
default CABS-dock mode and using its advanced options that enable the user to
increase the range of flexibility for chosen receptor fragments or to exclude
user-selected binding modes from docking search. Furthermore, we demonstrate a
strategy to improve CABS-dock performance by assessing the quality of models
with classical molecular dynamics. Finally, we discuss the promising extensions
and applications of the CABS-dock method and provide a tutorial appendix for
the convenient analysis and visualization of CABS-dock results. The CABS-dock
web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/
