Publications by authors named "Darrin York"

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SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations.
Tai-Sung Lee, Omid Jahanmahin, Saikat Pal, Darrin M York

J Phys Chem B· 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, Darrin M York

J Chem Inf Model· August 2025

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FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks.
Timothy J Giese, Ryan Snyder, Zeke Piskulich, German P Barletta, Shi Zhang, Darrin M York

J Chem Inf Model· June 2025

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Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications.
Timothy J Giese, Jinzhe Zeng, Darrin M York

J Phys Chem B· June 2025

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Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction.
Manju Ojha, Lucia Hudson, Amanda Photenhauer, Trinity Zang, Lauren Lerew, Darrin M York

Nucleic Acids Res· June 2025

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DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials.
Jinzhe Zeng, Duo Zhang, Anyang Peng, Xiangyu Zhang, Sensen He, Darrin M York

J Chem Theory Comput· May 2025

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DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials.
Jinzhe Zeng, Timothy J Giese, Duo Zhang, Han Wang, Darrin M York

J Chem Inf Model· April 2025

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The QDπ dataset, training data for drug-like molecules and biopolymer fragments and their interactions.
Jinzhe Zeng, Timothy J Giese, Andreas W Götz, Darrin M York

Sci Data· April 2025

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Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA.
Manju Ojha, Lucia Hudson, Amanda Photenhauer, Trinity Zang, Lauren Lerew, Darrin M York

bioRxiv· February 2025

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DPA-2: a large atomic model as a multi-task learner.
Duo Zhang, Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Darrin M York

NPJ Comput Mater· December 2024

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The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.
Timothy J Wilson, Erika McCarthy, Şölen Ekesan, Timothy J Giese, Nan-Sheng Li, Darrin M York

ACS Catal· October 2024

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Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.
Hsu-Chun Tsai, James Xu, Zhenyu Guo, Yinhui Yi, Chuan Tian, Darrin M York

J Chem Inf Model· September 2024

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Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields.
Timothy J Giese, Jinzhe Zeng, Lauren Lerew, Erika McCarthy, Yujun Tao, Darrin M York

J Phys Chem B· July 2024

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Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions.
Yuxuan Wu, Shi Zhang, Darrin M York, Lu Wang

J Phys Chem B· July 2024

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Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials.
Yujun Tao, Timothy J Giese, Şölen Ekesan, Jinzhe Zeng, Bálint Aradi, Darrin M York

J Chem Phys· June 2024

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Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials.
Yujun Tao, Timothy J Giese, Darrin M York

Molecules· June 2024

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Alchemical Enhanced Sampling with Optimized Phase Space Overlap.
Shi Zhang, Timothy J Giese, Tai-Sung Lee, Darrin M York

J Chem Theory Comput· May 2024

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Surface-Accelerated String Method for Locating Minimum Free Energy Paths.
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York

J Chem Theory Comput· March 2024

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Modern Alchemical Free Energy Methods for Drug Discovery Explained.
Darrin M York

ACS Phys Chem Au· November 2023

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AmberTools.
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, G Andrés Cisneros, Darrin M York

J Chem Inf Model· October 2023

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DeePMD-kit v2: A software package for deep potential models.
Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Darrin M York

J Chem Phys· August 2023

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Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.
Suhyun Yoon, Edward Ollie, Darrin M York, Joseph A Piccirilli, Michael E Harris

Biochemistry· July 2023

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Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.
Erika McCarthy, Şölen Ekesan, Timothy J Giese, Timothy J Wilson, Jie Deng, Darrin M York

Nucleic Acids Res· May 2023

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Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations.
Timothy J Giese, Darrin M York

J Chem Phys· May 2023

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Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states.
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York

J Chem Phys· March 2023

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