Any Ideas about Covalent bond btw ligand and protein residue?

PaddlePaddle / PaddleHelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

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Any Ideas about Covalent bond btw ligand and protein residue? #323

Closed YaoYinYing closed 1 month ago

YaoYinYing commented 1 month ago

I would like to add some features like creating covalent bond between input ligand and protein atom(with similar way of treating leaving groups from protein like rosettafold-all-atom) or harmonic distance constraints from one to anther in order to mimic such bonding info. Any ideas?

RyanGarciaLI commented 1 month ago

Hi,

Our opensource model doesn't directly support covalent bond input, but you may create an input adapter to implement it. Firstly, please refer to a cif file with covalent bonds and find out asym_id, seq_id, atom_id for all covalent connections. Next, try to put those features into make_bond_features() in ./helixfold/data/pipeline_conf_bonds.py. This function explains how HelixFold3 integrates with covalent bond features.

Thanks

YaoYinYing commented 1 month ago

@RyanGarciaLI Thanks so much for this message you provided! I have implemented this function in my branch and it looks good to me!