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Surface Amino-Acid From Sequence Only

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 protein
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updated by Jan Kosinski Jan Kosinski • written by Sheila Sheila

3 answers

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:

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updated by Ram Ram • written by Jan Kosinski Jan Kosinski

is Jnet downloadable?

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written by Sheila Sheila

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

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written by João Rodrigues João Rodrigues

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".

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written by Neilfws Neilfws

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

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written by Sheila Sheila

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.

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written by Keith Callenberg Keith Callenberg

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

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written by Neilfws Neilfws

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

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written by Keith Callenberg Keith Callenberg

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

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written by Keith Callenberg Keith Callenberg

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

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written by Michael Kuhn Michael Kuhn

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

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written by Sheila Sheila

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

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written by Michael Kuhn Michael Kuhn

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

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written by Sheila Sheila

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