Solvent- Accessible Surface Area

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6.6 years ago

bushranazir.333 ▴ 10

I am working on protein docking. I want to extract the coordinates of the surface atoms i.e coordinates of the atoms on the accessible surface area. I want to use python coding only and I dont want to rely on any other software.

Can anyone please guide me about the approach? Does Biopython have tools for this?

protein docking Python Surface Atoms Biopython • 3.1k views

ADD COMMENT • link 6.6 years ago by bushranazir.333 ▴ 10

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Biopython module for DSSP seems to do that http://biopython.org/DIST/docs/api/Bio.PDB.DSSP%27-module.html

ADD REPLY • link 6.6 years ago by microfuge ★ 1.9k

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I dont think that it deals with the coordinates of surface atoms.

ADD REPLY • link 6.6 years ago by bushranazir.333 ▴ 10

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If you could convince yourself to use JAVA and jmol, then you may find this of use: http://jmol.sourceforge.net/docs/surface/

ADD REPLY • link 6.5 years ago by Kevin Blighe 87k

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I am restricted to use python only

ADD REPLY • link 6.5 years ago by bushranazir.333 ▴ 10

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