Alchemical prediction of hydration free energies for SAMPL. - David L. Mobley; Shaui Liu; David S. Cerutti; William C. Swope; Julia E. Rice (J. Comput. Aided Mol. Des., 2012)

On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. - Nupur Bansal; Zheng Zheng 002; David S. Cerutti; Kenneth M. Merz Jr. (J. Comput. Aided Mol. Des., 2017)

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)

AmberTools. - David A. Case; Hasan Metin Aktulga; Kellon Belfon; David S. Cerutti; G. Andrés Cisneros; Vinícius Wilian D. Cruzeiro; Negin Forouzesh; Timothy J. Giese; Andreas W. Götz; Holger Gohlke; Saeed Izadi; Koushik Kasavajhala; et al. (J. Chem. Inf. Model., 2023)

Recent Developments in Amber Biomolecular Simulations. - David A. Case; David S. Cerutti; Vinícius Wilian D. Cruzeiro; Thomas A. Darden; Robert E. Duke; Mahdieh Ghazimirsaeed; George M. Giambasu; Timothy J. Giese; Andreas W. Götz; Julie A. Harris; Koushik Kasavajhala; Tai-Sung Lee; et al. (J. Chem. Inf. Model., 2025)