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Why does DeepPocket not predict residues for some fpocket pockets? #35

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JavierSanchez-Utges opened this issue Apr 23, 2024 · 0 comments

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@JavierSanchez-Utges
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JavierSanchez-Utges commented Apr 23, 2024

Hi, I was trying DeepPocket on chain B of 1a5h and tried to segment ALL pockets predicted by fpocket. I have noticed that out of the 14 predicted by fpocket, only 3 have been segmented (I have removed the lines that break the loop when count >= 3. In this example, it is pockets 1, 3, and 10, which correspond to fpocket 2, 1, and 5, respectively. I have checked and there are no predicted residues:

Pocket 11 of 1a5h_B has [] predicted residues
Pocket 12 of 1a5h_B has [] predicted residues
Pocket 13 of 1a5h_B has [] predicted residues
Pocket 14 of 1a5h_B has [] predicted residues
Pocket 15 of 1a5h_B has [] predicted residues
Pocket 16 of 1a5h_B has [] predicted residues
Pocket 17 of 1a5h_B has [] predicted residues

And this is how masks_pred look like:

        [[0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         ...,
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.]],

        [[0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         ...,
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.]],

        [[0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         ...,
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.],
         [0., 0., 0.,  ..., 0., 0., 0.]]])

Any idea why this is? I would expect a pocket could be segmented out of each fpocket prediction. Thanks!

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