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Published 20 hours ago • verified publisher icon flatironinstitute

Error in saliency maps

Open ga01 opened this issue 2 years ago • 4 comments

Dear DeepFRI developers, There seems to be an error in the saliency maps when the latest release and the downloadable models are used. For example in the case of 2PE5 in the Nat. Comms paper for the DNA-binding GO term (GO:0003677) the DNA-binding domain of the protein is activated (~1-50 residues, Figure 4C), but with the current version of the tool and models, residues that are not involved in DNA-binding are activated: saliency_fig_2PE5-B_GO 0003677

Best wishes, George

ga01 avatar Feb 14 '23 17:02 ga01

PS.: It seems that when using the new models, all three proteins (2w83-E, 2J9H-A, 2PE5-B) of Figure 4C of the DeepFRI paper (https://doi.org/10.1038/s41467-021-23303-9) have saliency maps that do not match the pattern on Figure 4C, and also does not correspond with the ligand binding residues.

I wonder whether it would be possible to provide also the original models that were used in the paper for download?

ga01 avatar Feb 15 '23 16:02 ga01

Excuse me, but how are the activation sites of BioLip added to the graph? Where is the data where to download it?

MiJia-ID avatar Nov 30 '23 03:11 MiJia-ID

image

MiJia-ID avatar Nov 30 '23 03:11 MiJia-ID

Excuse me, but how are the activation sites of BioLip added to the graph? Where is the data where to download it?

I also want to ask this question, can anyone provide an answer?

Young0222 avatar Aug 13 '24 07:08 Young0222