Re: [ccp4bb] Pisa application

[Edwin Pozharski]

On 08/08/2012 09:00 AM, Jose Duarte wrote:

To my knowledge PISA by itself is not able to do interface prediction


To my understanding PISA is not *intended* to do interface prediction

[ccp4bb] Pisa application

[Careina Edgooms]

Dear ccp4ers

I just wonder whether anybody knows if the PISA software could be used/modified 
to detect potential interfaces of interaction of different proteins? This would 
be very useful as a tool to validate protein-protein interactions detected by 
in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, 
does anyone know of other software that could do a similar thing?

Best
Careina 

Re: [ccp4bb] Pisa application

[Steiner, Roberto]

Maybe

Nat 
Protoc.http://www.ncbi.nlm.nih.gov/pubmed?term=Predicting%20protein-protein%20interactions%20on%20a%20proteome%20scale%20by%20matching%20evolutionary%20and%20structural%20similarities%20at%20interfaces%20using%20PRISM#
 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367.
Predicting protein-protein interactions on a proteome scale by matching 
evolutionary and structuralsimilarities at interfaces using PRISM.
Tuncbag 
Nhttp://www.ncbi.nlm.nih.gov/pubmed?term=Tuncbag%20N%5BAuthor%5Dcauthor=truecauthor_uid=21886100,
 Gursoy 
Ahttp://www.ncbi.nlm.nih.gov/pubmed?term=Gursoy%20A%5BAuthor%5Dcauthor=truecauthor_uid=21886100,
 Nussinov 
Rhttp://www.ncbi.nlm.nih.gov/pubmed?term=Nussinov%20R%5BAuthor%5Dcauthor=truecauthor_uid=21886100,
 Keskin 
Ohttp://www.ncbi.nlm.nih.gov/pubmed?term=Keskin%20O%5BAuthor%5Dcauthor=truecauthor_uid=21886100.
Source
Center for Computational Biology and Bioinformatics, College of Engineering, 
Koc University, Rumelifeneri Yolu, Sariyer Istanbul, Turkey.
Abstract
Prediction of protein-protein interactions at the structural level on the 
proteome scale is important because it allows prediction of protein function, 
helps drug discovery and takes steps toward genome-wide structural systems 
biology. We provide a protocol (termed PRISM, protein interactions bystructural 
matching) for large-scale prediction of protein-protein interactions and 
assembly of protein complex structures. The method consists of two components: 
rigid-body structural comparisons of target proteins to known template 
protein-protein interfaces and flexible refinement using a docking energy 
function. The PRISM rationale follows our observation that globally different 
protein structures can interact via similar architectural motifs.PRISM predicts 
binding residues by using structural similarity and evolutionary conservation 
of putative binding residue 'hot spots'. Ultimately,PRISM could help to 
construct cellular pathways and functional, proteome-scale annotation. PRISM is 
implemented in Python and runs in a UNIX environment. The program accepts 
Protein Data Bank-formatted protein structures and is available at 
http://prism.ccbb.ku.edu.tr/prism_protocol/.


On 8 Aug 2012, at 07:33, Careina Edgooms wrote:

Dear ccp4ers

I just wonder whether anybody knows if the PISA software could be used/modified 
to detect potential interfaces of interaction of different proteins? This would 
be very useful as a tool to validate protein-protein interactions detected by 
in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, 
does anyone know of other software that could do a similar thing?

Best
Careina

Roberto Steiner
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Pisa application

[Jose Duarte]

Hi Careina

To my knowledge PISA by itself is not able to do interface prediction. 
In any case there are a few methods available for protein-protein 
interface prediction. See for example this nice compilation:


http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/

Hope it helps

Jose


On 08/08/2012 08:33 AM, Careina Edgooms wrote:

Dear ccp4ers

I just wonder whether anybody knows if the PISA software could be 
used/modified to detect potential interfaces of interaction of 
different proteins? This would be very useful as a tool to validate 
protein-protein interactions detected by in vivo methods such as yeast 
2 hybrid screens. If PISA is not quite there yet, does anyone know of 
other software that could do a similar thing?


Best
Careina

Re: [ccp4bb] Pisa application

[David Waterman]

Perhaps IBIS does what you want?
http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi

IBIS ... infers/predicts interacting partners and binding sites by homology


-- David


On 8 August 2012 07:33, Careina Edgooms careinaedgo...@yahoo.com wrote:

 Dear ccp4ers

 I just wonder whether anybody knows if the PISA software could be
 used/modified to detect potential interfaces of interaction of different
 proteins? This would be very useful as a tool to validate protein-protein
 interactions detected by in vivo methods such as yeast 2 hybrid screens. If
 PISA is not quite there yet, does anyone know of other software that could
 do a similar thing?

 Best
 Careina

Re: [ccp4bb] Pisa application

[Xun Lu]

Hi Careina,

 I asked the exactly same question in this year's CCP4 summer school @APS, 
and the answer I got was no ... PISA is not for predicting 



Cheers,

Xun


Sent from my iPad

On Aug 8, 2012, at 2:33 AM, Careina Edgooms careinaedgo...@yahoo.com wrote:

 Dear ccp4ers
 
 I just wonder whether anybody knows if the PISA software could be 
 used/modified to detect potential interfaces of interaction of different 
 proteins? This would be very useful as a tool to validate protein-protein 
 interactions detected by in vivo methods such as yeast 2 hybrid screens. If 
 PISA is not quite there yet, does anyone know of other software that could do 
 a similar thing?
 
 Best
 Careina