Re: [ccp4bb] protein interactions
Search for homologous binding partners with close or remote homologies with your own sequences can also be addressed from the InterEvol database http://biodev.cea.fr/interevol/ It seems you can upload the sequences there : http://biodev.cea.fr/interevol/interevalign.aspx Hope this can help Marie-Ln Dr Marie-Hélène LeDu Laboratoire de Biologie Structurale et Radiobiologie CEA/DSV/IBiTec-S, CEA Saclay Bât 144, pièce 25 91191 Gif-sur-Yvette, France Tel : 33 (0)1 69 08 71 35 E-mail : marie-helene.l...@cea.fr Le 06/09/12 14:20, « moham...@strubi.ox.ac.uk » moham...@strubi.ox.ac.uk a écrit : 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
[ccp4bb] protein interactions
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
Re: [ccp4bb] protein interactions
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
Re: [ccp4bb] protein interactions
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 ---BeginMessage--- 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 ---End Message---
Re: [ccp4bb] protein interactions
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, moham...@strubi.ox.ac.uk 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 careinaedgo...@yahoo.comwrote: 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: j-kell...@northwestern.edu ***
