This new paper describes our ClusPro web server, a widely used tool for protein-protein docking. ClusPro provides a simple interface for basic use, but it also offers a number of advanced options to modify the search. These include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Applications of ClusPro include docking X-ray or NMR structures of proteins, modeling antibody-antigen interactions, constructing the structure of multidomain proteins, building homo-oligomers, peptide docking, homology model docking, and more.
