Publications by authors named "Daniel Roe"

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Spin-Polarized Nonferromagnetic Surfaces for Electrocatalysis: Chemo-Spintronics.
Hansaem Jang, Daniel Roe, Harry E Taylor, Emiliano Poli, Alex S Walton

J Am Chem Soc· December 2025

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Recent Developments in Amber Biomolecular Simulations.
David A Case, David S Cerutti, Vinícius Wilian D Cruzeiro, Thomas A Darden, Robert E Duke, Daniel R Roe

J Chem Inf Model· August 2025

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CADENCE: Clustering Algorithm─Density-Based Exploration and Novelty Clustering with Efficiency.
Lexin Chen, Daniel R Roe, Ramón Alain Miranda-Quintana

J Chem Inf Model· July 2025

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Extended Quality (eQual): Radial Threshold Clustering Based on -ary Similarity.
Lexin Chen, Micah Smith, Daniel R Roe, Ramón Alain Miranda-Quintana

J Chem Inf Model· May 2025

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CADENCE: Clustering Algorithm - Density-based Exploration and Novelty Clustering with Efficiency.
Lexin Chen, Daniel R Roe, Ramón Alain Miranda-Quintana

bioRxiv· February 2025

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Extended Quality (eQual): Radial threshold clustering based on n-ary similarity.
Lexin Chen, Micah Smith, Daniel R Roe, Ramón Alain Miranda-Quintana

bioRxiv· December 2024

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modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.
Olivia Love, Rodrigo Galindo-Murillo, Daniel R Roe, Pablo D Dans, Thomas E Cheatham Iii

J Chem Theory Comput· November 2024

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CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Wonmuk Hwang, Steven L Austin, Arnaud Blondel, Eric D Boittier, Stefan Boresch, Daniel R Roe

J Phys Chem B· October 2024

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k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations.
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda-Quintana

J Chem Theory Comput· July 2024

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'A kindergarten teacher must have 100 eyes and 100 ears!': Kindergarten teachers' experiences coping with child sexual abuse and problematic sexual behavior.
Laura I Sigad, Noah Bar Gosen, Limor Golan, Efrat Lusky-Weisrose, Jordan Shaibe, Daniel Roe

Child Abuse Negl· May 2024

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MPI-parallelization of the grid inhomogeneous solvation theory calculation.
Daniel R Roe, Bernard R Brooks

J Comput Chem· April 2024

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k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations.
Lexin Chen, Daniel R Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda-Quintana

bioRxiv· March 2024

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International consensus statement on the design, delivery and evaluation of sport-based interventions aimed at promoting social, psychological and physical well-being in prison.
Conor Murray, Brendan Coyle, Haydyn Morgan, Ian Marder, David Woods, Daniel Roe

BMJ Open· January 2024

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AmberTools.
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, G Andrés Cisneros, Daniel R Roe

J Chem Inf Model· October 2023

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Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories.
Daniel R Roe, Bernard R Brooks

Protein Sci· December 2022

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Methodological reflections on artistically illustrating ethnographic text from a study of sport pedagogy in youth detention: Ethics, affect, and description.
Daniel Roe, Åsa Bäckström

Front Sports Act Living· November 2022

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School principals coping with child sexual abuse in their schools.
Dafna Tener, Efrat Lusky-Weisrose, Daniel Roe, Roni Mor, Laura I Sigad

Child Abuse Negl· July 2022

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prepareforleap: An automated tool for fast PDB-to-parameter generation.
Daniel R Roe, Christina Bergonzo

J Comput Chem· May 2022

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Improving the speed of volumetric density map generation via cubic spline interpolation.
Daniel R Roe, Bernard R Brooks

J Mol Graph Model· May 2021

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Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory.
Lieyang Chen, Anthony Cruz, Daniel R Roe, Andrew C Simmonett, Lauren Wickstrom

J Chem Theory Comput· May 2021

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Sleep, Noninvasive Brain Stimulation, and the Aging Brain: Challenges and Opportunities.
Sara M Romanella, Daniel Roe, Rachel Paciorek, Davide Cappon, Giulio Ruffini

Ageing Res Rev· August 2020

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A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations.
Daniel R Roe, Bernard R Brooks

J Chem Phys· August 2020

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Protonation state of the selectivity filter of bacterial voltage-gated sodium channels is modulated by ions.
Ana Damjanovic, Ada Y Chen, Robert L Rosenberg, Daniel R Roe, Xiongwu Wu

Proteins· March 2020

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Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].
Alan Grossfield, Paul N Patrone, Daniel R Roe, Andrew J Schultz, Daniel W Siderius

Living J Comput Mol Sci· October 2018

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Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data.
Daniel R Roe, Thomas E Cheatham

J Comput Chem· September 2018

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