Question: Sequence Based Protein Interaction Information
3
gravatar for pixie@bioinfo
10.1 years ago by
pixie@bioinfo1.4k
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

I wanted to know if there is any tool which can predict protein interaction based on sequence alone...(I don't have any ids for the sequence).

kindly help...

ADD COMMENTlink modified 10.1 years ago by Reyhaneh480 • written 10.1 years ago by pixie@bioinfo1.4k

It is not clear to me what you mean by "I don't have any ids for the sequence" ? Is it just sequenced in your lab ?

ADD REPLYlink written 10.1 years ago by Khader Shameer18k

its just a domain...and it has got a pfam id...

ADD REPLYlink written 10.1 years ago by pixie@bioinfo1.4k

are the PPI predictions to be based on PPI data for orthologues of your sequences?

ADD REPLYlink written 9.4 years ago by Russh1.2k
4
gravatar for Perry
10.1 years ago by
Perry290
philadelphia
Perry290 wrote:

You might want to check out this cautionary paper, which claims

simple sequence-based features contain insufficient information to be useful for predicting protein-protein interactions, but that protein domain-based features have some predictive value.

ADD COMMENTlink written 10.1 years ago by Perry290

thaks for the reply

ADD REPLYlink written 10.1 years ago by pixie@bioinfo1.4k
3
gravatar for Neilfws
10.1 years ago by
Neilfws49k
Sydney, Australia
Neilfws49k wrote:

Yes, there are quite a lot of sequence-based methods to predict PPI. Their accuracy varies widely, depending on the method used and the quality of training data. Did you have a particular protein family in mind?

I'd start at PubMed with a search for "protein-protein interaction prediction sequence" - currently 289 results (162 freely-available and 26 reviews).

ADD COMMENTlink written 10.1 years ago by Neilfws49k

thanks for ur reply..

ADD REPLYlink written 10.1 years ago by pixie@bioinfo1.4k
3
gravatar for Lars Juhl Jensen
10.1 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

Depending on what exactly you mean by "predict from sequence alone", you might want to try STRING. It allows you to query with a sequence (or more sequences if you like) in order to retrieve a protein interaction network. Just starting from sequences (and no IDs) it will thus allow you get a predicted interaction network. However, the underlying evidence is based on numerous other things than just the sequences that you queried with, and I am thus not sure if it is what you are looking for.

ADD COMMENTlink written 10.1 years ago by Lars Juhl Jensen11k

thanks for ur reply....I did try for strings..

ADD REPLYlink written 10.1 years ago by pixie@bioinfo1.4k
0
gravatar for Khader Shameer
10.1 years ago by
Manhattan, NY
Khader Shameer18k wrote:

If you are looking at Human, Yeast or Rat proteins, you may try PIP: Potential Interactions of Proteins. Manuscript describing PIP method is available here.

ADD COMMENTlink written 10.1 years ago by Khader Shameer18k

thanks for the link..

ADD REPLYlink written 10.1 years ago by pixie@bioinfo1.4k
0
gravatar for Burlappsack
9.4 years ago by
Burlappsack660
Burlappsack660 wrote:

You might have better luck using gene ontologies and looking at expression patterns rather than trying to predict a structure, then further predict is likely binding sites.

ADD COMMENTlink written 9.4 years ago by Burlappsack660
0
gravatar for Reyhaneh
9.2 years ago by
Reyhaneh480
United Kingdom
Reyhaneh480 wrote:

This is one of the starting points of predicting protein protein interaction : Server: http://csbg.cnb.csic.es/mtserver/ References: http://pdg.cnb.uam.es/pazos/mirrortree/ I like the way these people have start from a simple idea in 2000 and are still working on it. the last paper is 2010 talks about Context Mirror Tree.

There are so many different ways to predict PPI using only sequence information. the new methods have integrated Classification methods, Bayesian framework into their work. have a look at this paper for example:http://www.ncbi.nlm.nih.gov/pubmed/17360525

also look at this for specific organism: http://cic.scu.edu.cn/bioinformatics/predict_ppi/default.html

There are also works on predicting PPI combining 3D structure information with sequence.

ADD COMMENTlink written 9.2 years ago by Reyhaneh480
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