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?
As much as I understood you think that a peptide fragment in the 60 AA part in protein x which is not modeled interacts with protein y in dimeric state. To see if a peptide fragment from the protein x will interact with dimeric y, you can model different peptide fragments and model it on dimeric y ( provided you know the binding site approximately). You can use sliding window approach to see which part among this 60 AA region gives best score. You can also choose the fragments from the 60 AA acids part after modeling it. From my experience 60 AA is too large for FlexPepDock to model unless you have well derived constraints.
Best of luck.