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)

Roughness of Molecular Property Landscapes and Its Impact on Modellability. - Matteo Aldeghi; David E. Graff; Nathan C. Frey; Joseph A. Morrone; Edward O. Pyzer-Knapp; Kirk E. Jordan; Connor W. Coley (J. Chem. Inf. Model., 2022)

Self-Focusing Virtual Screening with Active Design Space Pruning. - David E. Graff; Matteo Aldeghi; Joseph A. Morrone; Kirk E. Jordan; Edward O. Pyzer-Knapp; Connor W. Coley (J. Chem. Inf. Model., 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)

SPARK: Harnessing Human-Centered Workflows with Biomedical Foundation Models for Drug Discovery. - Bum Chul Kwon; Simona Rabinovici-Cohen; Beldine Moturi; Ruth Mwaura; Kezia Wahome; Oliver Njeru; Miguel Shinyenyi; Catherine Wanjiru; Sekou L. Remy; William Ogallo; Itai Guez; Parthasarathy Suryanarayanan; et al. (IJCAI, 2024)

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)

Multi-view biomedical foundation models for molecule-target and property prediction. - Parthasarathy Suryanarayanan; Yunguang Qiu; Shreyans Sethi; Diwakar Mahajan; Hongyang Li; Yuxin Yang; Elif K. Eyigöz; Aldo Guzmán-Sáenz; Daniel E. Platt; Timothy H. Rumbell; Kenney Ng; Sanjoy Dey; et al. (CoRR, 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)