Hi,
I have a problem. The two residues in the protein structure are not connected, which causes the short section to appear separate from the protein. This results in a visible gap in the RMSD and RMSF graphs.
I predicted a protein with high confidence. I tried to replace the ligand where it was, but it was not exactly where I wanted it. That's why I want to use the original X-ray one. How can I prevent it from appearing as a gap in the RMSD and RMSF graph? After all, this is a matter of the stability of the complex.
Normally, this means that that some parts of the structure was too mobile and therefore not resolved in the structure. You can model in these loops, but need to be aware that they do not have a single defined conformation in aqueous solution of the protein.
Article Current approaches to flexible loop modeling
Article New Deep Learning Methods for Protein Loop Modeling
https://academic.oup.com/bib/article/25/1/bbad486/7505239
I processed to fill the gap using a modeller to make the loop in the Chimere software. Now, it is ready for the MD process. I ll monitor the exact results in RMSD and RMSF plots
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