Author

Kunyang Sun

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Open access Aug 2026

LinkLlama: Enabling a Large Language Model for Chemically Reasonable Linker Design.

Fragment-based drug discovery (FBDD) relies heavily on the design of chemically viable linkers to connect fragments binding to different pocket regions into potent lead molecules. While recent generative models have advanced spatial fragment linking, they frequently produce linkers characterized by high torsional strai...

Kun-Yang Sun, Ying-Ze Wang, Justin Purnomo et al. · Journal of Chemical Informat... · 0 citations

#protein folding Open access Sep 2026

A curated benchmark for cofolding models on kinase conformational states

KinConfBench is introduced, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states.

Kun-Yang Sun, T. Head-Gordon · npj Drug Discovery · 0 citations

Open access Jul 2026

CAFE: A Co-folding Approach for Fragment Exploration of Allosteric and Cryptic Binding Sites

Co-folding models hold immense potential for allosteric drug discovery, but have been severely hampered by their systematic bias toward orthosteric ligand binding. While fragment screening has been proposed for allosteric binding site discovery, we show that co-folding models still suffer from memorization in which che...

Justin Purnomo, Kunyang Sun, T. Head-Gordon · bioRxiv · 0 citations