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radifar / PyPLIF-HIPPOS

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS
https://pyplif-hippos.readthedocs.io
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Failed to identify the hydrogen interaction in 5ikq #12

Open EmanuelD1989 opened 3 months ago

EmanuelD1989 commented 3 months ago

I am using Hippos-genref to identify finger print interactions in COX-2 (PDB: ID 5IKQ). I am only using two residues (TYR 353 and SER530) for the input. The result's bitstring is 00100000000000. According to the other fingerprint analysis, hydrogen interaction are presented for both residues. However, Hippos failed to identify them.

enade-istyastono commented 1 month ago

Could you please provide the config file and the final version of the protein and ligand file with hydrogens?

I've checked using PLANTS and SPORES to prepare the protein and ligand files and found the same result. Visual inspection using YASARA showed that the angle between the hydroxyl group from SER530 and the O from the ligand acceptor could not form the hydrogen interaction. Please see the picture below. The step of adding the hydrogen played an important role here. Btw, there's no TYR 353. So I used TYR 355. image