h-MINT improves ligand-protein binding affinity prediction by 2-4% and virtual screening metrics by 1-3% via overlapping fragment tokenization and hierarchical modeling.
Equivariant graph neural networks for 3d macromolecular structure.arXiv preprint arXiv:2106.03843
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Diversity-regularized DPO fine-tuning of ProteinMPNN improves structural similarity scores by at least 8% over base model and sequence diversity by up to 20% over standard DPO for peptide inverse folding on OpenFold structures.
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h-MINT: Modeling Pocket-Ligand Binding with Hierarchical Molecular Interaction Network
h-MINT improves ligand-protein binding affinity prediction by 2-4% and virtual screening metrics by 1-3% via overlapping fragment tokenization and hierarchical modeling.
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Improving Inverse Folding for Peptide Design with Diversity-regularized Direct Preference Optimization
Diversity-regularized DPO fine-tuning of ProteinMPNN improves structural similarity scores by at least 8% over base model and sequence diversity by up to 20% over standard DPO for peptide inverse folding on OpenFold structures.