Question regarding buried or exposed residues

[Anonymous]

Dear all,

I’d really like to know which application can define the residues of a protein to be burrei or exposed in Rosetta3.4. I could not find this piece of information in the manual. I need your help to introduce the details including the commond and related flags(I find some thing at http://www.rosettacommons.org/content/question-regarding-mlipo-score , but I didn’t konw it meets my requirement and how the .lips4 file is produced).
Thanks for your help.

[Anonymous]

1)Is my description of the problem not clear, or I have other mistake. Couble you please give me some tips, Thank you.
2)I simply study the Rosetta3.4 code, founding that there are some mention of buried rusidues. Because I still not familiar with the Rosetta framework, I do not know which place can be used as the interface. hoping to get your help.
Best Regards!

[Anonymous]

The Mlipo and .lps4 stuff is for membrane proteins – for soluble or globular proteins you can safely ignore it.

I’m not quite sure what you’re looking for. You talk about *defining* residues as buried or exposed – are you trying to fold a protein with extra information about where each residue is, or do you already have a folded protein structure which you want to classify the various residues? Also, what do you mean by “place can be used as the interface”? Are you trying to specify or force a given interface for docking, search for a possible interface, or are you trying to analyze an interface in an existing complex?

Regarding scoring interfaces, the best application we have is the InterfaceAnalyzer http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/df/dc8/_interface_analyzer_doc.html

[Anonymous]

My poor English bring you some troubles, so sorry! I talk about *defining* residues as buried or exposed – are I alredy have a folded structure which I want to classify the various residues which are buried or exposed. How can I get the information with Rosetta’s application. Thank you very much.

[Anonymous]

Interestingly, I can’t seem to find a released application which will easily yield this information. Typically, people use one of two metrics to find that sort of information – either the solvent accessible surface area (sasa) or the number of neighbors (how many residues are within a given distance, typically 10 Ang is used). While both can be calculated in the code, neither is directly exposed by commandline applications, at least as far as I can see (there may be some program that outputs the values incidentally, but none which output it as a major function).

If you want to hack the code or use PyRosetta, you can get access to the sasa information from core::scoring::calc_per_atom_sasa() (the per residue sasa will be returned in the passed rsd_sasa vector). The number of neighbors for a residue should be available from pose.energies().tenA_neighbor_graph().get_node( resnum )->num_neighbors_counting_self() after the pose has been scored.

[Anonymous]

Thank you for your patiently, it’s fruitful for me.

[Author]

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