How to analyze the output of flex ddG (example2: single site saturation mutagenesis)

[daipayans]

Hi @kylebarlow, Please advise on how to analyze the output of single site saturation mutagenesis after running the program, analyze_flex_ddG.py. The stdout to the terminal (or redirecting to a log) includes information for 1 out of 20 possible muations. However, in the directory, analysis_output, a csv file (output_saturation-results.csv) containing the ddG scores for all 20 possible mutations are included.

I notice that this file records the ddG scores multiple times for the same mutation (for e.g. F__Y is repeated 8 times) and similar for all other 19 amino acids. Should I average the value of the last backrub step accross multiple repeats or is it already averaged in the last step?

Thanks in advance for your help! -Daipayan

[Sh-Yana]

Hello, thank you for the wonderful program!

I have the same question - should I average the ddG values across backrub steps, or should I just take the ddG value from the very last step of a backrub trajectory (please see the image attached)? Could anyone answer please? :) @kylebarlow @flychcken @entropybit @jhcloos

Thank you! Yana

[entropybit]

I am a bit confused, why is that addressed to me as well ? But I hope one of the developers will be able to help you soon.