BindingDB: Amino acid sequences and y_pred values #16

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opened 2025-10-14 17:38:21 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:38:21 -06:00

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Originally created by @jchen634 on 7/4/2023

Dear DeepPurpose team,

Thank you so much for providing this powerful tool! I am new to this field and would like to ask some basic questions if you don't mind.
Here, I am trying to predict the binding affinity between the small compound of interest and the short peptide sequence using the Transformer+CNN_BindingDB model.

While, even if I change the input of the amino acid sequence to either very long >100 a.a. or very short, just one amino acid, the y_pred value is always around 5.3~5.7, which is not a significant difference. The output is pKd, correct? If yes, then the bin
Also, I have changed the y value, but it does not affect the y_pred at all. Is it normal, and what is the function of y here?

Thank you in advance.

*Originally created by @jchen634 on 7/4/2023* Dear DeepPurpose team, Thank you so much for providing this powerful tool! I am new to this field and would like to ask some basic questions if you don't mind. Here, I am trying to predict the binding affinity between the small compound of interest and the short peptide sequence using the Transformer+CNN_BindingDB model. While, even if I change the input of the amino acid sequence to either very long >100 a.a. or very short, just one amino acid, the y_pred value is always around 5.3~5.7, which is not a significant difference. The output is pKd, correct? If yes, then the bin Also, I have changed the y value, but it does not affect the y_pred at all. Is it normal, and what is the function of y here? Thank you in advance. ![image](https://github.com/kexinhuang12345/DeepPurpose/assets/88463596/6e0b089e-42ba-493e-a5ef-7d2c5816b273)

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Reference: github/DeepPurpose#16

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