Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver

Protein-protein and protein-DNA/RNA interactions are involved in many cellular processes. Therefore, determining their complex structures at the atomic level is valuable to gain insights into these interactions. Because of the technical difficulties and high cost in experimental methods, computational approaches like molecular docking have been developed to predict the structures of macromolecular complexes in the last decades. To automatically integrate the available binding information from the PDB, we have developed HDOCK, a protein-protein/nucleic acid docking web server by combining template-based and free docking. In this chapter, we first briefly introduce our HDOCK server and then give a step-by-step description of docking bovine chymotrypsinogen A against its inhibitor (PDB ID: 1CGI). Two case studies of realistic examples are also discussed. The HDOCK server is freely available at http://hdock.phys.hust.edu.cn/ .