I only know basic theory to predict protein-protein interaction by computational method (to construct network) such as gene fusion prediction and protein docking. Could anyone suggest links to suitable literature?
I have sequences of protein A, B, C, D, E, F, G and H which are involved in cell cycle. What should I do to predict the interaction between these proteins by computational method? Please suggest a method or computational protocol other than protein-protein docking.
I am actually trying to learn the methods where we could predict the protein interaction between the two proteins by computational method e.g. In theory it says that if we find two genes A and B fused in one genome, similar A and B gene occurs in other genome as separate entity. This is an indication that both A and B protein interact with each other. So prediction is done on this property of Gene fusion (I know just theory). I want to know how it is done computationally.
You can try PDBsum. It gives you the nice list and graphical representation of all the interaction taking part among the protein subunits.
Dear Rahu
You can find what you need in InterProSurf website.
http://curie.utmb.edu/prosurf.html
or
Olink
http://www.olink.com/products-services/duolink/applications/protein-interactions
Hi Rahu,
Have look at the following paper. It gives an excellent overview of the data and methods that can be used to infer protein protein interactions.
Assessing the limits of genomic data integration for predicting protein networks
Long J. Lu, Yu Xia, Alberto Paccanaro, Haiyuan Yu, and Mark Gerstein
Genome Res. 2005. 15: 945-953
http://genome.cshlp.org/content/15/7/945.full
Note that methods based gene fusion events are limited in their predictive power to cases where fusion event data is available. I myself used Gene Ontology annotation with good success. See the following paper for details and a link to the prediction software:
Gene Ontology-driven inference of protein-protein interactions using inducers.
Bioinformatics. 2012 Jan 1;28(1):69-75. Epub 2011 Nov 4.
Maetschke SR, Simonsen M, Davis MJ, Ragan MA.
http://www.ncbi.nlm.nih.gov/pubmed/22057159
Thank you Mohamed Abdel Gawwad and Tanima Shree for your response.
THANK YOU, Stefan Maetschke for giving me links and reference, It was really helpful. I will be going through the references and literature u send me.
STRING: http://string-db.org/newstring_cgi/show_input_page.pl?UserId=S6_Oyj2akqxs&sessionId=gwGCs8WGAnx2
For example I use it for pre evaluation of potential functions of unknown protein and identification of its possible partners, by substituting sequence in well-studied proteome (of course as an approximate method in the initial stage of research).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375030/?tool=pubmed
find out on this site may get required info
thank u
In 2008, Petre et al published the review "Computational Methods For Predicting Protein–Protein Interactions" (DOI 10.1007/10_2007_089) that is very interesting. I don't know if there is anything more up to date.
THANK YOU Parvel Karpov, Rajashri Bhairamadgi and Mario Guarracino for your informative response...
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology