Computational Analysis of Phosphopeptide Binding to the Polo-Box Domain of the Mitotic Kinase PLK1 Using Molecular Dynamics Simulation. - David J. Huggins; Grahame J. McKenzie; Daniel D. Robinson; Ana J. Narváez; Bryn Hardwick; Meredith Roberts-Thomson; Ashok R. Venkitaraman; Guy H. Grant; Mike C. Payne (PLoS Comput. Biol., 2010)

Benchmarking the thermodynamic analysis of water molecules around a model beta sheet. - David J. Huggins (J. Comput. Chem., 2012)

Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules. - Kamran Haider; David J. Huggins (J. Chem. Inf. Model., 2013)

Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation. - David J. Huggins (J. Comput. Chem., 2014)

Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties. - Alexander D. Wade; Lee-Ping Wang; David J. Huggins (J. Chem. Inf. Model., 2018)

Computational Fluorine Scanning Using Free-Energy Perturbation. - Alexander D. Wade; Andrea Rizzi; Yuanqing Wang; David J. Huggins (J. Chem. Inf. Model., 2019)

Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method. - Alexander D. Wade; David J. Huggins (J. Chem. Inf. Model., 2020)

Enhancing Hit Discovery in Virtual Screening through Absolute Protein-Ligand Binding Free-Energy Calculations. - Wei Chen; Di Cui; Steven V. Jerome; Mayako Michino; Eelke B. Lenselink; David J. Huggins; Alexandre Beautrait; Jeremie Vendome; Robert Abel; Richard A. Friesner; Lingle Wang (J. Chem. Inf. Model., 2023)

Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation. - Shan Sun; Makoto Fushimi; Thomas Rossetti; Navpreet Kaur; Jacob Ferreira; Michael Miller; Jonathan Quast; Joop van den Heuvel; Clemens Steegborn; Lonny R. Levin; Jochen Buck; Robert W. Myers; et al. (J. Chem. Inf. Model., 2023)

Addition to "Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation". - Shan Sun; Makoto Fushimi; Thomas Rossetti; Navpreet Kaur; Jacob Ferreira; Michael Miller; Jonathan Quast; Joop van den Heuvel; Clemens Steegborn; Lonny R. Levin; Jochen Buck; Robert W. Myers; et al. (J. Chem. Inf. Model., 2024)

Comparing Molecules Generated by MMPDB and REINVENT4 with Ideas from Drug Discovery Design Teams. - Shan Sun; David J. Huggins (J. Chem. Inf. Model., 2025)