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. 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

Acyl-homoserine lactone (AHL) quorum sensing enables many species of proteobacteria to coordinate collective behaviors. In such systems, a synthase produces an AHL signal, which is sensed by a LuxR-family receptor. Despite extensive genomic annotation of LuxR homologs, preferred AHLs for most receptors remain unknown,...

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