In Silico Binding Free Energy Predictability by Using the Linear Interaction Energy (LIE) Method: Bromobenzimidazole CK2 Inhibitors as a Case Study. - Andrea Bortolato; Stefano Moro (J. Chem. Inf. Model., 2007)

Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. - Andrea Bortolato; Benjamin G. Tehan; Michael S. Bodnarchuk; Jonathan W. Essex; Jonathan S. Mason (J. Chem. Inf. Model., 2013)

Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF1R as a Test Case. - Andrea Bortolato; Francesca Deflorian; Dahlia R. Weiss; Jonathan S. Mason (J. Chem. Inf. Model., 2015)

GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking. - Dahlia R. Weiss; Andrea Bortolato; Benjamin G. Tehan; Jonathan S. Mason (J. Chem. Inf. Model., 2016)

Reaction-Based Enumeration, Active Learning, and Free Energy Calculations To Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin-Dependent Kinase 2 Inhibitors. - Kyle D. Konze; Pieter H. Bos; Markus K. Dahlgren; Karl Leswing; Ivan Tubert-Brohman; Andrea Bortolato; Braxton Robbason; Robert Abel; Sathesh Bhat (J. Chem. Inf. Model., 2019)

On Ternary Complex Stability in Protein Degradation: In Silico Molecular Glue Binding Affinity Calculations. - Dahlia R. Weiss; Andrea Bortolato; Yongnian Sun; Xianmei Cai; Chon Lai; Sixuan Guo; Lihong Shi; Veerabahu Shanmugasundaram (J. Chem. Inf. Model., 2023)

Directional ΔG Neural Network (DrΔG-Net): A Modular Neural Network Approach to Binding Free Energy Prediction. - Derek P. Metcalf; Zachary L. Glick; Andrea Bortolato; Andy Jiang; Daniel L. Cheney; C. David Sherrill (J. Chem. Inf. Model., 2024)