Finding Binding Site Residues

Question

[antoniaa]

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.

[Michael]

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

[antoniaa]

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?

Answer 1

[Mensur Dlakic]

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.

• https://www.ebi.ac.uk/thornton-srv/m-csa/
• http://www.ebi.ac.uk/pdbsum
• http://sts.bioe.uic.edu/castp/index.html
• http://bioinfo-pharma.u-strasbg.fr/scPDB/

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

• http://cbm.bio.uniroma2.it/pdbinder/
• https://github.com/pulimeng/DeepDrug3D
• https://gitlab.com/cheminfIBB/kalasanty

Answer 2

[Jiyao Wang]

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