modeller_usage

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modeller_usage@salilab.org

March 2023

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2 discussions

Negative molpdf values
by Isabel Elliott 23 Mar '23

23 Mar '23

Hi, I am generating and refining models using the LoopModel or DOPELoopModel or DOPEHRLoopModel methods. Sometimes I get negative molpdf values for some of my generated models. What does this mean? I thought that the molpdf should be positive. The models with the most negative molpdf correspond to the most negative (i.e the lowest) DOPE scores - are these therefore the best models? Thanks.

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Design of a chmieric protein from two known structures
by dafnikarr＠gmail.com 15 Mar '23

15 Mar '23

Hello , i want to design a chimeric protein by fusion of subdomains of two known proteins. Do you know how should write the relevant scripts? And how to do the alignment? Should i use the multi template approach and use the two proteins as a template? Thank you! Dafni

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