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How To Calculate Rasa Of Proteins By Residue?

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?

structural-bioinformatics
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updated by Jiyao Wang • Jiyao Wang • written by tesni • tesni

3 answers

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.

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written by João Rodrigues João Rodrigues

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

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written by Khader Shameer Khader Shameer

@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?

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written by tesni • tesni

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..

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written by João Rodrigues João Rodrigues

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

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written by Jiyao Wang • Jiyao Wang

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