Makes sense now, thank you!

Mariana

________________________________ From: Min-yi Shen minyishen@gmail.com Sent: Friday, June 19, 2020 5:27:08 PM To: Modeller Caretaker Cc: Mariana GONZALEZ MEDINA; modeller_usage@salilab.org Subject: Re: [modeller_usage] z-DOPE score

Original DOPE author here. The Z-dope is effectively an estimated z-score of your protein model based on the protein composition and size, as the raw DOPE scores are size and protein dependent. Z-dope used a linear model to estimate the mean and sd of a protein’s DOPE score based on their sizes and compositions. It was trained by millions of models from ModBase. -1.5 means your model’s DOPE score is -1.5 standard deviation lower than the average... usually a good indicator of good native overlap.

I can’t believe I can still recall all these...

On Thu, Jun 18, 2020 at 11:59 Modeller Caretaker <modeller-care@salilab.orgmailto:modeller-care@salilab.org> wrote: On 6/18/20 9:48 AM, Mariana GONZALEZ MEDINA wrote: > I have a question regarding the zDOPE score. I have read some paper that > state this: "The Z-DOPE scores ranged from −1.63 to −1.85, where a score > of less than −1 indicates a “reliable” model (i.e., 80% of its Cα atoms > are within 3.5 Å of their correct positions)" > > I am wondering how is it that a score of less than -1 indicates that 80% > of its Cα atoms are within 3.5 Å of their correct positions?

I would say "implies" rather than "indicates". DOPE is a model evaluation function. Of course we don't know the true structure so we can only guess with some degree of confidence (the more negative the score, the more confident I would be) whether a good DOPE score really means a correct model. Benchmarking does show that this is typically the case though; see the DOPE paper.

Ben Webb, Modeller Caretaker -- modeller-care@salilab.orgmailto:modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage _______________________________________________ modeller_usage mailing list modeller_usage@salilab.orgmailto:modeller_usage@salilab.org https://salilab.org/mailman/listinfo/modeller_usage