[Chimera-users] How do I find the active site?

[Elaine Meng]

Hi Abryn,
There is no “predict active site” feature in Chimera.  However, you can use various tools in Chimera to get information to help you guess which is the active site.   For example, you could

(1) show the pockets and tunnels found from the shape of the protein by CASTp
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>

If the structure isn’t already in the PDB and the CASTp database, you could use the CASTp website directly as mentioned here:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010439.html>

(2) color the surface by hydrophobicity (e.g. if you know the ligand is hydrophobic) or electrostatic potential (if you know the ligand is charged).  Examples in tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

(3) open a sequence alignment that includes your protein, perhaps with others that also have the same function, and then color the structure based on the conservation in the sequence alignment.  I.e. highly conserved residues might be important for structure or function.  Examples in tutorial: <https://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 4, 2019, at 8:04 PM, Abryn Jeuness Luna <arluna at up.edu.ph> wrote:
> 
> Good day!
> 
> I am currently using UCSF Chimera for my protein structure analysis. However, I cannot find the active site of my protein structure. How do I find the active site, including the amino acids in it using UCSF Chimera? Thank you.
> 
> Regards,
> Abryn