How extract coordinates of surface atoms of a protein from a pdb file?
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7.7 years ago

Hi everyone,

I have a pdb file that contains a single protein information.

I want to extract the coordinates of the atoms that are on the surface of protein and by that I don't mean the set of atoms of surface residues because that set may contain atoms that are deeply buried inside the protein.

Is there any tool that can do this?

Thanks

atom surface pdb protein • 3.8k views
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7.7 years ago
João Rodrigues ★ 2.5k
Use NACCESS. It outputs both residue and atom accessibility.
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7.7 years ago

Adding to what João Rodrigues mentioned there is another free program (non commercial use) called MSMS that given a set of spheres S and a probe radius rp, computes the Reduced Surface and the analytical model of the Solvent Excluded Surface (SES).

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hello, I also want to extract all the residues on the surface of a PDB file. I agree to that people can do that by MSMS. But I do not kown why I cann't open the web www.scripps.edu/sanner/html/msms_man.html and download it. Can you give me a link which is available, or mail me(address: yuehuiy@mail.ustc.edu.cn).Thank you !

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7.7 years ago
venu 7.0k

Try in this way

• make a list of residues (3-letter code) which have high propensity to be on the surface (search literature).
• extract the coordinates of those residues.

Something like this will work.

$awk '$1=="ATOM"' pdbFile.pdb | grep -Fwf list | awk '{print$7"\t"$8"\t"$9}' > coOrdinates.txt  It extracts the coordinates of all surface residue atoms, you can extract only 'CA' atoms(represents a residue in coarse grained simu.) coordinates by modifying '$1=="ATOM" && \$3=="CA"'.

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Thank you but I said: "I don't mean the set of atoms of surface residues because that set may contain atoms that are deeply buried inside the protein."

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7.7 years ago
a.polo88 ▴ 110

I'm agree with Joao for the use of NACCCES. otherwise there are graphic molecular software e.g. swisswiev that have incorporated the module for calculate what do you ask.