There are several servers available based on fast Fourier transforms (FFTs). These servers are able to quickly carryout a global, grid-based matching searches.
Go to the ZDOCK server (http://zdock.bu.edu) and upload trypsin (2PTN) and its inhibitor (1BA7 chain B) for docking. Do this in groups in order to not overload the server. When the jobs have finished (typically under an hour), download the output file. You will have to also download a script for creating complexes from the output file. Use the script to generate the top five models.
Question: Are these models similar or diverse? How so? Are any of the models similar to the crystal structure of the bound complex (1AVW)?
(Other servers include SmoothDock (http://structure.pitt.edu/servers/smoothdock), ClusPro (http://cluspro.bu.edu),, Haddock (http://haddock.chem.uu.nl), and GRAMM-X (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx). Any of these provide global docking services to create models that might be useful for refinement by RosettaDock.)