Docking Flexible Molecules: A Case Study of Three Proteins. - Richard S. Judson; Y. T. Tan; E. Mori; C. Melius; Edward P. Jaeger; Adi M. Treasurywala; Alan M. Mathiowetz (J. Comput. Chem., 1995)

Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations. - Cristiano Ruch Werneck Guimarães; Alan M. Mathiowetz (J. Chem. Inf. Model., 2010)

Use of 3D Properties to Characterize Beyond Rule-of-5 Property Space for Passive Permeation. - Cristiano R. W. Guimarães; Alan M. Mathiowetz; Marina Shalaeva; Gilles Goetz; Spiros Liras (J. Chem. Inf. Model., 2012)

Exploring Aromatic Chemical Space with NEAT: Novel and Electronically Equivalent Aromatic Template. - Meihua Tu; Brajesh K. Rai; Alan M. Mathiowetz; Mary Didiuk; Jeffrey A. Pfefferkorn; Angel Guzman-Perez; John Benbow; Cristiano R. W. Guimarães; Scot Mente; Matthew M. Hayward; Spiros Liras (J. Chem. Inf. Model., 2012)

Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein-Ligand Complexes using ab Initio Calculations. - Brajesh K. Rai; Vishnu Sresht; Qingyi Yang; Raymond J. Unwalla; Meihua Tu; Alan M. Mathiowetz; Gregory A. Bakken (J. Chem. Inf. Model., 2019)

TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics. - Brajesh K. Rai; Vishnu Sresht; Qingyi Yang; Ray Unwalla; Meihua Tu; Alan M. Mathiowetz; Gregory A. Bakken (J. Chem. Inf. Model., 2022)