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Proteins|August 7, 2026
Unified Sampling and Ranking for Protein Docking With DFMDockLee-Shin Chu, Sudeep Sarma, Da Xu, et al.Biorxiv : the Preprint Server for Biology|October 10, 2024
Unified Sampling and Ranking for Protein Docking with DFMDockLee-Shin Chu, Sudeep Sarma, Jeffrey J GrayBiorxiv : the Preprint Server for Biology|December 15, 2025
Can We Extract Physics-like Energies from Generative Protein Diffusion Models?Sudeep Sarma, Harrison Truscott, Da Xu, et al.Biorxiv : the Preprint Server for Biology|December 11, 2025
Adapting Co-Folding Models for Structure-Based Protein-Protein Docking Through Flow MatchingDa Xu, Lee-Shin Chu, Jeffrey J GrayProteins|September 22, 2025
Docking With Rosetta and Deep Learning Approaches in CAPRI Rounds 47-55Ameya Harmalkar, Lee-Shin Chu, Samuel W Canner, et al.Biorxiv : the Preprint Server for Biology|June 22, 2026
ProtAff: Protein Binding Affinity Prediction via LoRA-Finetuned ESM-2Lee-Shin Chu, Jeff Vogt, Michael Chungyoun, et al.Protein Science : a Publication of the Protein Society|December 26, 2023
Flexible protein-protein docking with a multitrack iterative transformerLee-Shin Chu, Jeffrey A Ruffolo, Ameya Harmalkar, et al.Biorxiv : the Preprint Server for Biology|July 10, 2023
Flexible Protein-Protein Docking with a Multi-Track Iterative TransformerLee-Shin Chu, Jeffrey A Ruffolo, Ameya Harmalkar, et al.Nature Communications|May 15, 2023
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodiesJeffrey A Ruffolo, Lee-Shin Chu, Sai Pooja Mahajan, et al.Current Opinion in Structural Biology|March 21, 2006
High-resolution protein-protein dockingJeffrey J GrayPageof 77