Combining Docking Pose Rank and Structure with Deep Learning Improves Protein-Ligand Binding Mode Prediction over a Baseline Docking Approach. - Joseph A. Morrone; Jeffrey K. Weber; Tien Huynh; Heng Luo 002; Wendy D. Cornell (J. Chem. Inf. Model., 2020)

In-Pocket 3D Graphs Enhance Ligand-Target Compatibility in Generative Small-Molecule Creation. - Seung-gu Kang; Jeffrey K. Weber; Joseph A. Morrone; Leili Zhang; Tien Huynh; Wendy D. Cornell (CoRR, 2022)

Simplified, interpretable graph convolutional neural networks for small molecule activity prediction. - Jeffrey K. Weber; Joseph A. Morrone; Sugato Bagchi; Jan D. Estrada Pabon; Seung-gu Kang; Leili Zhang; Wendy D. Cornell (J. Comput. Aided Mol. Des., 2022)

Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational Autoencoder─Insights for Practical AI-Driven Molecule Generation. - Seung-gu Kang; Joseph A. Morrone; Jeffrey K. Weber; Wendy D. Cornell (J. Chem. Inf. Model., 2022)

Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity. - Jeffrey K. Weber; Joseph A. Morrone; Seung-gu Kang; Leili Zhang; Lijun Lang; Diego Chowell; Chirag Krishna; Tien Huynh; Prerana Parthasarathy; Binquan Luan; Tyler J. Alban; Wendy D. Cornell; et al. (Briefings Bioinform., 2024)

MAMMAL - Molecular Aligned Multi-Modal Architecture and Language. - Yoel Shoshan; Moshiko Raboh; Michal Ozery-Flato; Vadim Ratner; Alex Golts; Jeffrey K. Weber; Ella Barkan; Simona Rabinovici-Cohen; Sagi Polaczek; Ido Amos; Ben Shapira; Liam Hazan; et al. (CoRR, 2024)

Leveraging Large Language Models to Predict Antibody Biological Activity Against Influenza A Hemagglutinin. - Ella Barkan; Ibrahim Siddiqui; Kevin J. Cheng; Alex Golts; Yoel Shoshan; Jeffrey K. Weber; Yailin Campos Mota; Michal Ozery-Flato; Giuseppe A. Sautto (CoRR, 2025)