How to extract amino acids from receptor-ligand complex pdb?

Question

[mmarcell]

Hello everyone! What would be a good approach to extract amino acids from receptor-ligand complex pdb? I am only interested in the amino acid residues that interacts with the bound small molecule and it takes way to much time to manually visualize and write down the amino acids so I was wondering if there is an automated way.

I made molecular dockings with AutoDock4 and AutoDock Vina using a single small molecule and many different proteins which produced quite a lot of dlg and pdb outputs. I know how to visualize the bound conformation with AutoDock Tools and Discovery Studio and I also know how to make pdb files from dlgs.

Thank you for your help!

Answer 1

[Jiyao Wang]

You can use iCn3D and open your PDB file: structure.ncbi.nlm.nih.gov/icn3d. Then click the menu “select > by Distance”. You could also use the Node.js scripts as described at https://github.com/ncbi/icn3d/tree/master/icn3dnode