Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins. - Piotr Cieplak; Wendy D. Cornell; Christopher I. Bayly; Peter A. Kollman (J. Comput. Chem., 1995)

Calculation of Molecular Geometries, Relative Conformational Energies, Dipole Moments, and Molecular Electrostatic Potential Fitted Charges of Small Organic Molecules of Biochemical Interest by Density Function Theory. - Alain St.-Amant; Wendy D. Cornell; Peter A. Kollman; Thomas A. Halgren (J. Comput. Chem., 1995)

Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics. - Wendy D. Cornell; Maria P. Ha; Yax Sun; Peter A. Kollman (J. Comput. Chem., 1996)

Comparison of Topological, Shape, and Docking Methods in Virtual Screening. - Georgia B. McGaughey; Robert P. Sheridan; Christopher I. Bayly; J. Christopher Culberson; Constantine Kreatsoulas; Stacey Lindsley; Vladimir N. Maiorov; Jean-François Truchon; Wendy D. Cornell (J. Chem. Inf. Model., 2007)

Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results. - Robert P. Sheridan; Georgia B. McGaughey; Wendy D. Cornell (J. Comput. Aided Mol. Des., 2008)

QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets. - Robert P. Sheridan; Kiyean Nam; Vladimir N. Maiorov; Daniel R. McMasters; Wendy D. Cornell (J. Chem. Inf. Model., 2009)

Drug-like Density: A Method of Quantifying the "Bindability" of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank. - Robert P. Sheridan; Vladimir N. Maiorov; M. Katharine Holloway; Wendy D. Cornell; Ying-Duo Gao (J. Chem. Inf. Model., 2010)

Preface: Computational Technologies for Drug Discovery. - Wendy D. Cornell (IBM J. Res. Dev., 2018)

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)

Active Site Sequence Representations of Human Kinases Outperform Full Sequence Representations for Affinity Prediction and Inhibitor Generation: 3D Effects in a 1D Model. - Jannis Born; Tien Huynh; Astrid Stroobants; Wendy D. Cornell; Matteo Manica (J. Chem. Inf. Model., 2022)

On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction. - Jannis Born; Yoel Shoshan; Tien Huynh; Wendy D. Cornell; Eric J. Martin; Matteo Manica (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)