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It can be easily fixed by modifying all HID, HIE and HIP by HIS.
Is it a good way to fix it ? If it is the case, may be it could be done automatically in the inference code.
Otherwise, is there a way to read the PDB file that takes into account those variants of amino acids ?
PS-1 : When running DiffDock v1 on the same protein, everything is running fine. That's why I suspect the match of those modified histidines to X coming from the new package Prody.
PS-2 : I had this issue specifically with histidine, but may be it also happens with others amino acids ?
The text was updated successfully, but these errors were encountered:
Amber can give different names to histidine amino acid by examining which protons are present : HID, HIE, or HIP instead of HIS.
This raises an issue when featurizing the protein in Diffdock because those residues are matched to the one letter name
X
instead ofH
.DiffDock/datasets/constants.py
Line 3 in d3791a8
It can be easily fixed by modifying all HID, HIE and HIP by HIS.
Is it a good way to fix it ? If it is the case, may be it could be done automatically in the inference code.
Otherwise, is there a way to read the PDB file that takes into account those variants of amino acids ?
PS-1 : When running DiffDock v1 on the same protein, everything is running fine. That's why I suspect the match of those modified histidines to
X
coming from the new package Prody.PS-2 : I had this issue specifically with histidine, but may be it also happens with others amino acids ?
The text was updated successfully, but these errors were encountered: