I am currently trying to create a model using the flexpepdock algorithm. I currently have a structure that I have a lot of confidence in and I would like to extend one of the chains by 60 amion acids. The sequence of the current model, protein x, has been show to have interactions with protein y monomer (in our current model), however, there is about 60 amino acids of protein x that is not modeled. Under certain conditions protein y can form a dimer. my question is how do I extend protein x an additional 60 amino acids so that I can see if it has interactions with the second subunit of protein y. is there an application that will allow me to take a pdb that I have modeled and abintio flexpepdock the remaining amino acids to see if they can interact with the dimer version of protein y? and if so how do I use this 'merging algorithm'. I have read from this forum about a zone or template creator but I haven't found documentation on how to use this. I guess a better question is how do a model one protein using multiple algorithms?
Thanks for your help,