Question: Surface Amino-Acid From Sequence Only
5
gravatar for Sheila
8.7 years ago by
Sheila250
Germany
Sheila250 wrote:

I have some protein sequences and I wanted to know which amino-acid have more probability to be on surface.
Is there any tool which can predict surface residue from sequence only? Please tell me name of tools which can predict Surface accessibility of residue from sequence only.

I need tool which can be either downloadable or can be integrated in script easily.

protein • 2.3k views
ADD COMMENTlink modified 8.7 years ago by Jan Kosinski1.6k • written 8.7 years ago by Sheila250
4
gravatar for Jan Kosinski
8.7 years ago by
Jan Kosinski1.6k
Jan Kosinski1.6k wrote:

I use SSpro/ACCpro:

It is downloadable, easy to install and use, and complete in a sense that in brings all necessary databases with it.

Other, popular predictors that you can try:

ADD COMMENTlink modified 9 months ago by RamRS30k • written 8.7 years ago by Jan Kosinski1.6k

is Jnet downloadable?

ADD REPLYlink written 8.7 years ago by Sheila250

Here (http://www.compbio.dundee.ac.uk/www-jpred/legacy/jnet/) is sth but it may be old version, so I would ask the authors directly.

ADD REPLYlink modified 11 months ago by RamRS30k • written 8.7 years ago by Jan Kosinski1.6k
3
gravatar for João Rodrigues
8.7 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

You'll probably want to look for hydropathy plots instead. They won't be super reliable, but might give you a hint of which regions are exposed or not.

Expasy has plenty of resources for that: Link

A quick search on Pubmed yielded this that might be helpful.

Accuracy of protein hydropathy predictions

ADD COMMENTlink written 8.7 years ago by João Rodrigues2.5k

Hydropathy plots are not a good option for this purpose. As Michael says in his answer, there are lots of tools available and the keywords to find them are "solvent accessibility".

ADD REPLYlink written 8.7 years ago by Neilfws48k

of-course search for "solvent accessibility" gives available tools/papers. But I want to know which are widely used and more accurate.

ADD REPLYlink written 8.7 years ago by Sheila250

I agree that hydropathy plots alone will not answer the surface accessibility question, however the OP is looking for some information about the structure of a transmembrane protein, so some knowledge of which segments are TM is very important. Personally, I would run the sequence in TMHMM: http://www.cbs.dtu.dk/services/TMHMM/ before using a predictor like SSpro (mentioned above) so that I have a sense of the topology.

ADD REPLYlink written 8.7 years ago by Keith Callenberg910

I don't see any mention of transmembrane proteins in the original question.

ADD REPLYlink written 8.7 years ago by Neilfws48k

You're not looking at the original question. Sheila re-wrote it yesterday.

ADD REPLYlink written 8.7 years ago by Keith Callenberg910

Either the question has changed or it was originally tagged "transmembrane."

ADD REPLYlink written 8.7 years ago by Keith Callenberg910
2
gravatar for Michael Kuhn
8.7 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

Yes, there are such tools. You want to search for "solvent accessibility".

ADD COMMENTlink written 8.7 years ago by Michael Kuhn5.0k

of-course search for "solvent accessibility" gives available tools/papers. But I want to know which are widely used and more accurate.

ADD REPLYlink written 8.7 years ago by Sheila250

Then please put this in your original question. ;-) You asked "Is there any tool which can predict surface residue from sequence only?"

ADD REPLYlink written 8.7 years ago by Michael Kuhn5.0k

ok :) I rephrase my question 'Please tell me name of tools which can predict Surface accessibility of residue from sequence only !! :) '

ADD REPLYlink written 8.7 years ago by Sheila250
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