Daniel R. Roe

12 papers Journal 11Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
CADENCE: Clustering Algorithm─Density-Based Exploration and Novelty Clustering with Efficiency.
J. Chem. Inf. Model.
Lexin Chen, Daniel R. Roe, Ramón Alain Miranda-Quintana
2025 J jnl
Extended Quality (eQual): Radial Threshold Clustering Based on
J. Chem. Inf. Model.
Lexin Chen, Micah Smith, Daniel R. Roe, Ramón Alain Miranda-Quintana
2025 J jnl
Recent Developments in Amber Biomolecular Simulations.
J. Chem. Inf. Model.
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, Zhen Li, Charles Lin, Jian Liu, Yinglong Miao, Romelia Salomón-Ferrer, Jana Shen, Ryan Snyder, Jason M. Swails, Ross C. Walker, Jinan Wang, Xiongwu Wu, Jinzhe Zeng, Thomas E. Cheatham III, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
2024 J jnl
MPI-parallelization of the grid inhomogeneous solvation theory calculation.
J. Comput. Chem.
Daniel R. Roe, Bernard R. Brooks
2023 J jnl
AmberTools.
J. Chem. Inf. Model.
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, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
2022 J jnl
prepareforleap: An automated tool for fast PDB-to-parameter generation.
J. Comput. Chem.
Daniel R. Roe, Christina Bergonzo
2018 J jnl
Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data.
J. Comput. Chem.
Daniel R. Roe, Thomas E. Cheatham III
2017 — conf
Polyhedral Compilation Support for C++ Features: A Case Study with CPPTRAJ.
LCPC
Amit Roy, Daniel R. Roe, Mary W. Hall, Thomas E. Cheatham
2016 J jnl
Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Zahra Heidari, Daniel R. Roe, Rodrigo Galindo-Murillo, Jahan B. Ghasemi, Thomas E. Cheatham III
2015 J jnl
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis.
Comput. Sci. Eng.
Thomas E. Cheatham III, Daniel R. Roe
2014 J jnl
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing.
J. Cheminformatics
Julien C. Thibault, Daniel R. Roe, Julio C. Facelli, Thomas E. Cheatham III
2012 J jnl
Evaluation of DOCK 6 as a pose generation and database enrichment tool.
J. Comput. Aided Mol. Des.
Scott R. Brozell, Sudipto Mukherjee, Trent E. Balius, Daniel R. Roe, David A. Case, Robert C. Rizzo