Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. - Asim Okur; Bentley Strockbine; Viktor Hornak; Carlos Simmerling (J. Comput. Chem., 2003)

The Amber biomolecular simulation programs. - David A. Case; Thomas E. Cheatham III; Tom Darden; Holger Gohlke; Ray Luo 001; Kenneth M. Merz Jr.; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J. Woods (J. Comput. Chem., 2005)

Molecular mechanics parameters for the FapydG DNA lesion. - Kun Song; Viktor Hornak; Carlos De Los Santos; Arthur P. Grollman; Carlos Simmerling (J. Comput. Chem., 2008)

Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis. - Kevin Hauser; Yiqing He; Miguel Garcia-Diaz; Carlos Simmerling; Evangelos A. Coutsias (J. Chem. Inf. Model., 2017)

Laguerre-Intersection Method for Implicit Solvation. - Michelle Hatch Hummel; Bihua Yu; Carlos Simmerling; Evangelos A. Coutsias (Int. J. Comput. Geom. Appl., 2018)

Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4. - Junjie Zou; Chuan Tian; Carlos Simmerling (J. Comput. Aided Mol. Des., 2019)

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. - Lorenzo Casalino; Abigail C. Dommer; Zied Gaieb; Emília P. Barros; Terra Sztain; Surl-Hee Ahn; Anda Trifan; Alexander Brace; Anthony T. Bogetti; Austin Clyde; Heng Ma; Hyungro Lee; et al. (Int. J. High Perform. Comput. Appl., 2021)

SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. - Darya Stepanenko; Stephanie Budhan; Carlos Simmerling (J. Chem. Inf. Model., 2023)

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)

Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment. - Jason T. Linzer; Ethan Aminov; Aalim S. Abdullah; Colleen E. Kirkup; Rebeca I. Diaz Ventura; Vinay R. Bijoor; Jiyun Jung; Sophie Huang; Chi Gee Tse; Emily Álvarez Toucet; Hugo P. Onghai; Arghya P. Ghosh; et al. (J. Chem. Inf. Model., 2024)

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)