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.
Scoring function for automated assessment of protein structure template quality
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A multiscale optimization method using explicit protein backbone geometry reconstructs atomic models from cryo-EM data, showing improved RMSD and TM scores on three simulated datasets.
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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.
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Multiscale reconstruction of protein conformations from cryo-EM images
A multiscale optimization method using explicit protein backbone geometry reconstructs atomic models from cryo-EM data, showing improved RMSD and TM scores on three simulated datasets.