### Restricting TM-align to a given superposition

Posted:

**Wed Apr 03, 2024 1:29 am**Thank you for your continued development of the TM-align tool.

I am interested in using TM-align for a research project where I am comparing the local structural regions of proteins to eachother. For example, I might want to calculate the TM score between the atoms within a 20Å radius of a "centre" residue S100, and another set of atoms surrounding residue S200.

Given that I know that the two serine residues should be "centred" on top of eachother (i.e. their respective atomic coordinates should be (0,0,0)), I would like to evaluate the TM score for the two "spheres" of atoms, but I would like to restrict the TM-align algorithm to only consider finding the optimal rotation during the structural alignment. This is because I want to enforce that the two centre Serine residues are superimposed in the same space and find an optimal pairing of all other atoms around these residues.

I assume something like this is possible given the dynamic programming approach of the algorithm, where combinations of which residues are superimpose to which (in the 2nd structure) are explored.

Thank you in advance.

I am interested in using TM-align for a research project where I am comparing the local structural regions of proteins to eachother. For example, I might want to calculate the TM score between the atoms within a 20Å radius of a "centre" residue S100, and another set of atoms surrounding residue S200.

Given that I know that the two serine residues should be "centred" on top of eachother (i.e. their respective atomic coordinates should be (0,0,0)), I would like to evaluate the TM score for the two "spheres" of atoms, but I would like to restrict the TM-align algorithm to only consider finding the optimal rotation during the structural alignment. This is because I want to enforce that the two centre Serine residues are superimposed in the same space and find an optimal pairing of all other atoms around these residues.

I assume something like this is possible given the dynamic programming approach of the algorithm, where combinations of which residues are superimpose to which (in the 2nd structure) are explored.

Thank you in advance.