MUFold-Contact and TPCref: New Methods for Protein Structure Contact Prediction and Refinement. - Jeffrey A. Ruffolo; Zhaoyu Li; Yi Shang (BIBM, 2019)

Geometric potentials from deep learning improve prediction of CDR H3 loop structures. - Jeffrey A. Ruffolo; Carlos Guerra; Sai Pooja Mahajan; Jeremias Sulam; Jeffrey J. Gray (Bioinform., 2020)

Deciphering antibody affinity maturation with language models and weakly supervised learning. - Jeffrey A. Ruffolo; Jeffrey J. Gray; Jeremias Sulam (CoRR, 2021)

ProGen2: Exploring the Boundaries of Protein Language Models. - Erik Nijkamp; Jeffrey A. Ruffolo; Eli N. Weinstein; Nikhil Naik 002; Ali Madani (CoRR, 2022)

Antibody structure prediction using interpretable deep learning. - Jeffrey A. Ruffolo; Jeremias Sulam; Jeffrey J. Gray (Patterns, 2022)

Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion. - Alex Morehead; Jeffrey A. Ruffolo; Aadyot Bhatnagar; Ali Madani (CoRR, 2024)

Conditional Enzyme Generation Using Protein Language Models with Adapters. - Jason Yang; Aadyot Bhatnagar; Jeffrey A. Ruffolo; Ali Madani (CoRR, 2024)