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jertubiana / ScanNet

Apache License 2.0
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Detect active sites of enzymes that binding and catalyzing substrate? #5

Closed BinhongLiu closed 1 year ago

BinhongLiu commented 1 year ago

Hi, Really nice tool! Could ScanNet be used to detect active sites of an enzyme that bind and catalyze substrates? Thanks!

jertubiana commented 1 year ago

Hi Hongbin, Thank you for your interest in our research. In principle, yes, ScanNet is suitable to detect active sites. Extended Data Figure 7d shows that the learnt amino acid representation captures the convexity of the molecular surface, which is a key property of active sites. You would need to fine-tune the model on a dedicated training set. Best, Jérôme

On 15 Jan 2023, at 13:47, Hongbin Liu @.***> wrote:

Hi, Really nice tool! Could ScanNet be used to detect active sites of an enzyme that bind and catalyze substrates? Thanks!

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BinhongLiu commented 1 year ago

Thanks for your prompt reply! Yes, I agree that fine-tuning the model on a dedicated training set will be better. Since preparing the dedicated training set may take me some time. I'd like to use the current model directly, though I'm not sure how much the predictions for the active site will be affected using the current model. Thanks again.