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.
Pifold: Toward effective and efficient protein inverse folding
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SurfDesign introduces surface-conditioned protein design via manifold modeling and equivariant message passing on surfaces integrated with pretrained language models, outperforming prior methods on binder and enzyme design benchmarks.
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.
citing papers explorer
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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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SurfDesign: Effective Protein Design on Molecular Surfaces
SurfDesign introduces surface-conditioned protein design via manifold modeling and equivariant message passing on surfaces integrated with pretrained language models, outperforming prior methods on binder and enzyme design benchmarks.
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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.