Script to list residues within a given distance from ligand

Question

[miromoman]

Hello,

Is anyone aware of a simple Linux program or script that provides a list of protein residues with at least one atom located at a certain distance from a ligand?

I have done this many times with PyMol or Chimera, among others, but now I do not need a fancy GUI, just some simple code that returns a list of residues.

Best regards,

Miro

[Collin]

I've also had to do neighbor searching through a script. In my case I created my own python script using the Biopython library (guide here), which handles PDB parsing for you. I ended up using neighbor = Bio.PDB.NeighborSearch(atoms) (where atoms is a list of Biopython atom objects) object and calling the neighbor.search_all(radius, level='R') method. That returned all pairs of residues with at least one atom within some radius distance. I then filtered the pairs for what I was looking for. So if creating your own script is an option, then Biopython might be helpful.

[miromoman]

Thank you. I have ended up using Binana (http://nbcr.ucsd.edu/data/sw/hosted/binana/) which is a bit of an overkill but gets the job done and I might end up using it also for more sophisticated purposes.

Answer 1

[Khader Shameer]

Please try HORI: Higher Order Residue Interactions in Proteins.

Link to webserver here: http://caps.ncbs.res.in/hori/

Manuscript here: http://www.ncbi.nlm.nih.gov/pubmed/20122196

Disclaimer: I am co-author of this work.

Answer 2

[wpwupingwp]

In pymol, you can select residues around one molecular like this:

select name,molecular around 5

Answer 3

[db4]

Pytraj is a possibility. You can load you load your file into pytraj and use the atom selection to select residues around distance from ligand. https://amber-md.github.io/pytraj/latest/atom_mask_selection.html