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Finding Binding Site Residues

Edited!!

Dear all,

I need to find binding site residues of a protein that is bound a ligand. How can I extract these residues from VMD or PDB file?

Thanks.

protein residue binding site
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updated by Jiyao Wang • Jiyao Wang • written by antoniaa • antoniaa

This question needs to be more specific: binding sites for what?, do you want to predict de-novo or look up in a database?

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written by Michael Dondrup Michael Dondrup

Yes, you're right. I need to find the binding site residues of a protein bound to a ligand. I am wondering how I can extract these residues from PDB file or maybe VMD?

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written by antoniaa • antoniaa

2 answers

I am assuming you are asking about ligands in PDB structures, but you would help everyone by being more specific. For doing it on a small scale, I recommend LigPlot+ as described here.

If you are asking about binding site prediction, these may be of interest:

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written by Mensur Dlakic Mensur Dlakic

You can use a Node.js script based on iCn3D: https://github.com/ncbi/icn3d/tree/master/icn3dnode.

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written by Jiyao Wang • Jiyao Wang

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