I have used PyMol to model my structures, now I'm on the protein structure validation step and I preferred to use ERRAT, Verify3D and PROCHECK to validate my structures. Now I dont know how to interpret my results from the servers. Which values are indicatve of a good structure and what exactly should I be looking at on the server results?
Hi
You can check Ramachandran Plot from procheck and look for residues in favored regions and outliers. This will give you estimation about your model quality.
You can also check QMEANS server: https://swissmodel.expasy.org/qmean/help
Hope this helps
Regards
Pankaj
Pankaj Kumar Singh thank you so much for your help. Really appreciate it.
Pritam Kumar Panda
andManoj Kumar Gupta
thank you so much. Now I have an idea on how to go about. And that artcile will help me a lot I see. Thank you
Hi Zinhle,
These journal papers' might be helpful for you!
https://onlinelibrary.wiley.com/iucr/itc/Fb/ch21o3v0001/sec21o3o3o4/
https://www.sciencedirect.com/science/article/pii/S0076687997770228
https://scripts.iucr.org/cgi-bin/paper?gl0276
-Anik Banik
On verify3D, a score of more than 80% means that your model has good quality - however you must check with other evaluation tolls such as voromqa, Proq3 etc to make sure you have a high quality model.
might be helpful for you!
SAVESv6.0 - Structure Validation Server (ucla.edu)
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