How To Calculate Rasa Of Proteins By Residue?

Question

[tesni]

Hello all,

Is there any software available to calculate relative accessible surface area of proteins by residue from PDB IDs or from sequences? My dataset has 120 PDB ids. Is there any other methods available to do this calculation easily? I would like to use the following formula for rASA.

rASA = Predicted ASA / Standard ASA

Is any software available to get the ASA of all residues of my dataset (input: all PDB files or sequences) in a single time?

[Neilfws]

Suggest you click "similar posts" for answers to questions very similar to this; e.g. http://www.biostars.org/post/show/10650/defining-exposed-residues-from-dssp-solvent-accessibility-value/#10650

Answer 1

[João Rodrigues]

You could also take a look at NACCESS. Widely used, well accepted, and gives exactly what you ask for given one PDB file:

2) A residue accessibility (.rsa) file containing summed atomic accessible surface areas over each protein or nucleic acid residue, as well as the relative accessibility of each residue calculated as the %accessiblity compared to the accessibility of that residue type in an extended ALA-x-ALA tripeptide (for amino acids). See Hubbard, Campbell & Thornton (1991) J.Mol.Biol.220,507-530. You can prevent this file from being calculated if you don't need it.

Answer 2

[Khader Shameer]

JOY Package have a routine called psa. You can get ASA for all residues in a PDB file using psa. Details about JOY here.

[tesni]

@shameer Thank you very much for your answer. Here,the input is one PDB file. But my question is , can I give more than one pdb file as input?

[João Rodrigues]

I would say, as with any tool, write a for loop in bash or csh or whatever shell you use to process multiple structures. Easiest thing to do..

[tesni]

@Joao.Thanks for your comment. I am new to programming. That's why I am searching for ready made programs. I saw that WESA server can calculate solvent accessibility for multiple sequences. I couldn't use it because of error.I have asked about this in biostar . this is the link.http://www.biostars.org/post/show/42693/to-calculate-solvent-accessibility-with-wesa/. If you know about this , please help me.

Answer 3

[Jiyao Wang]

You could also use the command line script "surfacearea.js" based on iCn3D at https://github.com/ncbi/icn3d/tree/master/icn3dnode .