Hi Careina, For the first question, it sounds as though IBIS would do what you want: http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi. It will also try to answer your second question, although sequences are compared to known structures, so if your sequence is dissimilar to anything in the PDB it won't work. It looks as though you can only put in one query sequence/structure and will then have to scan the results for the appearance of the second.
I hope this helps. -- David On 6 September 2012 07:43, Careina Edgooms <careinaedgo...@yahoo.com> wrote: > Anybody know of any software out there that can predict potential > interaction sites between two proteins? They have been shown to interact > via y2h screens but I have no idea if they would interact on their own in > vitro. Before I clone them into a vector and purify them I would like some > sort of confirmation that the interaction could occur in the absence of > other cellular factors. > There are 2 interactions I am looking at. For the one, the structures of > both proteins are known. For the other only one structure is known. > So, is there software that uses 2 known structures to predict binding > sites and (I know this is a long shot), but is there any software around > that could predict an interaction based on the sequences only (or one 3D > structure and one sequence)? > > Thanks > Careina >
