Transformations and algorithms for least sum of squares hypersphere fitting. - Michael A. Burr; Alan C. Cheng; Ryan G. Coleman; Diane L. Souvaine (CCCG, 2004)

Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model. - Ryan G. Coleman; Anna C. Salzberg; Alan C. Cheng (J. Chem. Inf. Model., 2006)

Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility. - Kathryn A. Loving; Andy Lin; Alan C. Cheng (PLoS Comput. Biol., 2014)

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery. - Bradley Sherborne; Veerabahu Shanmugasundaram; Alan C. Cheng; Clara D. Christ; Renee L. DesJarlais; José S. Duca; Richard A. Lewis; Deborah A. Loughney; Eric S. Manas; Georgia B. McGaughey; Catherine E. Peishoff; Herman van Vlijmen (J. Comput. Aided Mol. Des., 2016)

Step Change Improvement in ADMET Prediction with PotentialNet Deep Featurization. - Evan N. Feinberg; Robert P. Sheridan; Elizabeth Joshi; Vijay S. Pande; Alan C. Cheng (CoRR, 2019)

Experimental Error, Kurtosis, Activity Cliffs, and Methodology: What Limits the Predictivity of Quantitative Structure-Activity Relationship Models? - Robert P. Sheridan; Prabha Karnachi; Matthew Tudor; Yuting Xu; Andy Liaw; Falgun Shah; Alan C. Cheng; Elizabeth Joshi; Meir Glick; Juan Alvarez (J. Chem. Inf. Model., 2020)

Exploring Deep Learning of Quantum Chemical Properties for Absorption, Distribution, Metabolism, and Excretion Predictions. - Megan A. Lim; Song Yang; Huanghao Mai; Alan C. Cheng (J. Chem. Inf. Model., 2022)

Denoising Drug Discovery Data for Improved Absorption, Distribution, Metabolism, Excretion, and Toxicity Property Prediction. - Matthew Adrian; Yunsie Chung; Alan C. Cheng (J. Chem. Inf. Model., 2024)

A call for an industry-led initiative to critically assess machine learning for real-world drug discovery. - Cas Wognum; Jeremy R. Ash; Matteo Aldeghi; Raquel Rodríguez-Pérez; Cheng Fang; Alan C. Cheng; Daniel J. Price; Djork-Arné Clevert; Ola Engkvist; W. Patrick Walters (Nat. Mac. Intell., 2024)

MolPROP: Molecular Property prediction with multimodal language and graph fusion. - Zachary A. Rollins; Alan C. Cheng; Essam Metwally (J. Cheminformatics, 2024)

Data Scaling and Generalization Insights for Medicinal Chemistry Deep Learning Models. - Jacky Chen; Yunsie Chung; Jonathan Tynan; Chen Cheng; Song Yang; Alan C. Cheng (J. Chem. Inf. Model., 2025)