Author

F. Dimaio

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Open access Sep 2026

RFOptimization: Guiding Design Optimization with All-Atom Structure Prediction

RFO formulates binder improvement as a residue-wise mutational search problem, sampling candidate substitutions alternately based on gradient-guided sequence optimization using all-atom structure prediction models and a cycling-based sequence redesign strategy that alternates structure generation with an orthogonal pre...

Odin Zhang, Jia-Qi Wang, T. R. Thompson et al. · bioRxiv · 0 citations

#protein folding Open access Sep 2026

COPAL: An ensemble of protein-ligand co-folding models enriches preferred ligand predictions for the LuxR-family of quorum sensing receptors

The COPAL (combining ordered predictions of audited ligands) pipeline, which integrates multiple protein-ligand co-folding models to identify preferred AHLs for a specific LuxR, shows that unweighted rank aggregation of complementary co-folding models offers a general strategy for predicting receptor-ligand specificity...

Davi Nakajima An, A. Schaefer, Szu-Min Chang et al. · bioRxiv · 0 citations