Measure Distances Between Aa Residues From An Msa Mapped To A Representative Protein Structure : To Find They Cluster Or Not

Question

[sayonidas03]

Hi,

I have a MSA and identified potentially functional important ones using Residue Conservation Score (calculated using Scorecons). Also I have a representative structure for these sequences. I need to find the distance between the important residues in the structure and infer whether they form clusters or not. Can you please advice me how to go about it? Are there any similar programs to measure distances between residues in a 3D structure or do I need to write my own script?. Any help/advice/suggestion is welcome. Many Thanks

Answer 1

[João Rodrigues]

I would write your own script for this, I cannot recall any software that does this. What you can do to avoid coding clustering algorithms is to get the residue numbers and just map them with PyMOL or VMD or Chimera or whatever other visualization program. This should give you a straightforward idea if they are clustered or not.

Also, with these programs, you can easily measure distances and write a very simple script (at least with pymol) to output them.