Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. - Daniel J. Mermelstein; Charles Lin; Gard Nelson; Rachael Kretsch; James Andrew McCammon; Ross C. Walker (J. Comput. Chem., 2018)

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. - Tai-Sung Lee; David S. Cerutti; Dan Mermelstein; Charles Lin; Scott LeGrand; Timothy J. Giese; Adrian E. Roitberg; David A. Case; Ross C. Walker; Darrin M. York (J. Chem. Inf. Model., 2018)

Improvements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular Dynamics Suite. - Daniel J. Mermelstein (2018)

FitScore: a fast machine learning-based score for 3D virtual screening enrichment. - Daniel K. Gehlhaar; Daniel J. Mermelstein (J. Comput. Aided Mol. Des., 2024)

Solvation and formal charge corrections to the Piecewise-Linear Potential. - Daniel K. Gehlhaar; Daniel J. Mermelstein (J. Comput. Aided Mol. Des., 2025)