How to optimize a protein structure in PyMol after adding phospho residues?

27 November 2023 1 8K Report

I am using PyMol with PyTMs plugin to visualize possible phosphorylation sites on a protein. I am wondering how I can use the program to calculate and show an optimized protein structure to avoid steric clashes.

Sambit Kumar Mishra

Not sure about pymol, but you can use available energy minimization servers such as Chiron (https://dokhlab.med.psu.edu/chiron/login.php)

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