I know this isn't exactly your question, but it doesn't really take that long to clone, express, and purify things nowadays--a few days, even? Also, won't you be doing this anyway? So why not cut out the middle-man? Or, better still, in your cloning downtime, do the software stuff.
JPK On Thu, Sep 6, 2012 at 7:20 AM, <[email protected]> wrote: > Hi Careina, > > In answer to your first question you could also try the iPATCH server: > > http://portal.stats.ox.ac.uk/userdata/proteins/i-Patch/home.pl > > This takes two reference structures for proteins that interact, and > combined with multiple sequence alignments of their homologs attempts to > predict the surface contact residues between them. > > As far as your second question is concerned, a quick google search using > the term "protein interaction prediction from sequence" gave some useful > links, one of which is Struct2Net: > > http://groups.csail.mit.edu/cb/struct2net/webserver/ > > This tool attempts to predict protein-protein interactions purely from > sequence data. However, it does use a structure-based threading approach, > so your sequences will be run against the pdb. If they are unique to > anything in the structural databases, it may not be useful. > > > Hope this helps, > > Mohammad > > > ---------------------------------------- > Dr. Mohammad W. Bahar > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > University of Oxford > > 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 <[email protected]>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 >> > > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [email protected] *******************************************
