I get a fail result for Verify3D option in SAVES almost every time for the structures designed. I would like to know is Molprobity score sufficient in terms of reliability for the purpose of molecular docking and MD simulations ?
The model that I am using is not from RCSB PDB resources. It is from alpha fold EMBL option. My question is whether after refining the structure, getting a failed result in Verify3D but fulfilling the molprobity score is sufficient to carry out the MD simulations or not. Yusuf Oloruntoyin Ayipo
Dear Joydeep, I am aware of the AlphaFold protein structures but I cannot tell about their validity since I haven't subjected any of them to test. I suggest you read more about the validation of their structures inArticle Highly accurate protein structure prediction with AlphaFold
. However, regarding your question, I will advise that you validate the structure model with other parameters in addition to molprobity comparatively with AlphaFold models. I think a good cumulative score in other parameters outside Verify 3D and consistent quality with AlphaFold counterpart could enhance the reliability of your model for molecular docking and MD.- Badges
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