Surface Amino-Acid From Sequence Only

Question

[Sheila]

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.

Answer 1

[Jan Kosinski]

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:

• Jnet
• Sable

[Sheila]

is Jnet downloadable?

[Jan Kosinski]

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.

Answer 2

[João Rodrigues]

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

[Neilfws]

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".

[Sheila]

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

[Keith Callenberg]

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.

[Neilfws]

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

[Keith Callenberg]

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

[Keith Callenberg]

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

Answer 3

[Michael Kuhn]

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

[Sheila]

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

[Michael Kuhn]

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

[Sheila]

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