Evaluation of DOCK 6 as a pose generation and database enrichment tool. - Scott R. Brozell; Sudipto Mukherjee 002; Trent E. Balius; Daniel R. Roe; David A. Case; Robert C. Rizzo (J. Comput. Aided Mol. Des., 2012)

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. - Julien C. Thibault; Daniel R. Roe; Julio C. Facelli; Thomas E. Cheatham III (J. Cheminformatics, 2014)

The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis. - Thomas E. Cheatham III; Daniel R. Roe (Comput. Sci. Eng., 2015)

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations. - Zahra Heidari; Daniel R. Roe; Rodrigo Galindo-Murillo; Jahan B. Ghasemi; Thomas E. Cheatham III (J. Chem. Inf. Model., 2016)

Polyhedral Compilation Support for C++ Features: A Case Study with CPPTRAJ. - Amit Roy; Daniel R. Roe; Mary W. Hall; Thomas E. Cheatham (LCPC, 2017)

Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. - Daniel R. Roe; Thomas E. Cheatham III (J. Comput. Chem., 2018)

prepareforleap: An automated tool for fast PDB-to-parameter generation. - Daniel R. Roe; Christina Bergonzo (J. Comput. Chem., 2022)

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)

MPI-parallelization of the grid inhomogeneous solvation theory calculation. - Daniel R. Roe; Bernard R. Brooks (J. Comput. Chem., 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)

CADENCE: Clustering Algorithm─Density-Based Exploration and Novelty Clustering with Efficiency. - Lexin Chen; Daniel R. Roe; Ramón Alain Miranda-Quintana (J. Chem. Inf. Model., 2025)

Extended Quality (eQual): Radial Threshold Clustering Based on n-ary Similarity. - Lexin Chen; Micah Smith; Daniel R. Roe; Ramón Alain Miranda-Quintana (J. Chem. Inf. Model., 2025)