Scores in generation_#_ranked.smi file

[Taylor Witte]

Hi!

We figured out that the first score is the ‘binding affinity’ from autodock. However, we have been struggling to figure out what the second score is and what it means. I was also wondering if you have any literature on this score.

Example: This is the first line from my ranked file what is the second score 9.512?
"[NH2+]=C(NNO)NC(O)=C1CC(CO)C1 (ZINC000104088847+ZINC000257828352)Gen_1_Mutant_13_921305 Gen_1_Mutant_13_921305 Gen_1_Mutant_13_921305__5 -6.7 9.512820878158223"

Best,
Taylor

[Jacob Durrant]

Hi Taylor. Much thanks for this question, and for your interest in AutoGrow4. I myself had a hard time finding the answer in the documentation. It’s buried in the TUTORIAL.md file: https://git.durrantlab.pitt.edu/jdurrant/autogrow4/-/blob/4.0.3/tutorial/TUTORIAL.md#providing-custom-plugins

...the last column is the diversity fitness and... the second to last column is the metric for "docking/rescored" fitness.

So just to clarify, the penultimate column is the affinity score (e.g., the Vina score), as you guessed. The last column is the diversity score. Here’s an explanation for how the diversity score is calculated, in case it helps: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00429-4#Sec9

Hope this helps. Take care.

~Jacob

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