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D

Darrin M. York

Rutgers University New Brunswick

62H-index
328Paper Count
5.5WCitation Count
Published Papers 132
Publication Date
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Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization
errJournal of Chemical Information and Modeling
IF5.3
err2026-03-09
err0
errOAAI
errAlejandro Blanco-Gonzalez; William Betancourt; Ryan Michael Snyder; Shi Zhang; Timothy J. Giese; Zeke A. Piskulich; Andreas W. Götz; Kenneth M. Merz Jr.; Darrin M. York; Hasan Metin Aktulga; Madushanka Manathunga
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A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules
errJournal of Chemical Information and Modeling
IF5.3
err2026-01-01
err0
PREAI
errTsai, Hsu-Chun; Zhang, Shi; Lee, Tai-Sung; Giese, Timothy J.; Lin, Charles; Xu, James; Yi, Yinhui; York, Darrin M.; Ganguly, Abir; Pan, Albert C.
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SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations
errThe Journal of Physical Chemistry B
IF2.9
err2025-12-09
err0
errOAAI
errTai-Sung Lee; Omid Jahanmahin; Saikat Pal; Darrin M. York
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Recent Developments in Amber Biomolecular Simulations
errJournal of Chemical Information and Modeling
IF5.3
err2025-07-29
err0
errOAAI
errDavid A. Case; David S. Cerutti; Vinícius Wilian D. Cruzeiro; Thomas A. Darden; Robert E. Duke; Mahdieh Ghazimirsaeed; George M. Giambaşu; Timothy J. Giese; Andreas W. Götz; Julie A. Harris; Koushik Kasavajhala; Tai-Sung Lee; Zhen Li; Charles Lin; Jian Liu; Yinglong Miao; Romelia Salomon-Ferrrer; Jana Shen; Ryan Snyder; Jason Swails; Ross C. Walker; Jinan Wang; Xiongwu Wu; Jinzhe Zeng; Thomas E. Cheatham III; Daniel R. Roe; Adrian Roitberg; Carlos Simmerling; Darrin M. York; Maria C. Nagan; Kenneth M. Merz Jr.
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Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications
errJOURNAL OF PHYSICAL CHEMISTRY B
IF2.9
err2025-05-26
err0
PREAI
errGiese, Timothy J.; Zeng, Jinzhe; York, Darrin M.
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FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2025-05-21
err0
errOAAI
errGiese, Timothy J.; Snyder, Ryan; Piskulich, Zeke; Barletta, German P.; Zhang, Shi; McCarthy, Erika; Ekesan, Solen; York, Darrin M.
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DPA-2: a large atomic model as a multi-task learner
errNPJ COMPUTATIONAL MATERIALS
IF11.9
err2024-12-19
err0
errOAAI
errZhang, Duo; Liu, Xinzijian; Zhang, Xiangyu; Zhang, Chengqian; Cai, Chun; Bi, Hangrui; Du, Yiming; Qin, Xuejian; Peng, Anyang; Huang, Jiameng; Li, Bowen; Shan, Yifan; Zeng, Jinzhe; Zhang, Yuzhi; Liu, Siyuan; Li, Yifan; Chang, Junhan; Wang, Xinyan; Zhou, Shuo; Liu, Jianchuan; Luo, Xiaoshan; Wang, Zhenyu; Jiang, Wanrun; Wu, Jing; Yang, Yudi; Yang, Jiyuan; Yang, Manyi; Gong, Fu-Qiang; Zhang, Linshuang; Shi, Mengchao; Dai, Fu-Zhi; York, Darrin M.; Liu, Shi; Zhu, Tong; Zhong, Zhicheng; Lv, Jian; Cheng, Jun; Jia, Weile; Chen, Mohan; Ke, Guolin; Weinan, E.; Zhang, Linfeng; Wang, Han
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The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme
errACS CATALYSIS
IF13.1
err2024-10-02
err0
errOAAI
errWilson, Timothy J.; McCarthy, Erika; Ekesan, Solen; Giese, Timothy J.; Li, Nan-Sheng; Huang, Lin; Piccirilli, Joseph A.; York, Darrin M.; Lilley, David M. J.
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Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-09-03
err0
PREAI
errTsai, Hsu-Chun; Xu, James; Guo, Zhenyu; Yi, Yinhui; Tian, Chuan; Que, Xinyu; Giese, Timothy; Lee, Tai-Sung; York, Darrin M.; Ganguly, Abir; Pan, Albert
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Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2024-06-10
err6
PREAI
errTao, Yujun; Giese, Timothy J.; Ekesan, Solen; Zeng, Jinzhe; Aradi, Balint; Ben Hourahine; Aktulga, Hasan Metin; Gotz, Andreas W.; Merz Jr, Kenneth M.; York, Darrin M.
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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
errMOLECULES
IF4.6
err2024-06-06
err2
errOAAI
errTao, Yujun; Giese, Timothy J.; York, Darrin M.
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Alchemical Enhanced Sampling with Optimized Phase Space Overlap
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-04-26
err5
PREAI
errZhang, Shi; Giese, Timothy J.; Lee, Tai-Sung; York, Darrin M.
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errSave
Surface-Accelerated String Method for Locating Minimum Free Energy Paths
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-02-17
err7
PREAI
errGiese, Timothy J.; Ekesan, Solen; McCarthy, Erika; Tao, Yujun; York, Darrin M.
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The AmberTools
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2023-10-08
err474
errOAAI
errCase, David A.; Aktulga, Hasan Metin; Belfon, Kellon; Cerutti, David S.; Cisneros, G. Andres; Cruzeiro, Vinicus Wilian D.; Forouzesh, Negin; Giese, Timothy J.; Gotz, Andreas W.; Gohlke, Holger; Izadi, Saeed; Kasavajhala, Koushik; Kaymak, Mehmet C.; King, Edward; Kurtzman, Tom; Lee, Tai-Sung; Li, Pengfei; Liu, Jian; Luchko, Tyler; Luo, Ray; Manathunga, Madushanka; Machado, Matias R.; Nguyen, Hai Minh; O'Hearn, Kurt A.; Onufriev, Alexey V.; Pan, Feng; Pantano, Sergio; Qi, Ruxi; Rahnamoun, Ali; Risheh, Ali; Schott-Verdugo, Stephan; Shajan, Akhil; Swails, Jason; Wang, Junmei; Wei, Haixin; Wu, Xiongwu; Wu, Yongxian; Zhang, Shi; Zhao, Shiji; Zhu, Qiang; Cheatham, I. I. I. Thomas E.; Roe, Daniel R.; Roitberg, Adrian; Simmerling, Carlos; York, Darrin M.; Nagan, Maria C.; Merz, Jr Kenneth M.
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Modern Alchemical Free Energy Methods for Drug Discovery Explained
errACS PHYSICAL CHEMISTRY AU
IF4.3
err2023-10-04
err34
errOAAI
errYork, Darrin M.
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errSave
DeePMD-kit v2: A software package for deep potential models
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2023-08-01
err153
errOAAI
errZeng, Jinzhe; Zhang, Duo; Lu, Denghui; Mo, Pinghui; Li, Zeyu; Chen, Yixiao; Rynik, Marian; Huang, Li'ang; Li, Ziyao; Shi, Shaochen; Wang, Yingze; Ye, Haotian; Tuo, Ping; Yang, Jiabin; Ding, Ye; Li, Yifan; Tisi, Davide; Zeng, Qiyu; Bao, Han; Xia, Yu; Huang, Jiameng; Muraoka, Koki; Wang, Yibo; Chang, Junhan; Yuan, Fengbo; Bore, Sigbjorn Loland; Cai, Chun; Lin, Yinnian; Wang, Bo; Xu, Jiayan; Zhu, Jia-Xin; Luo, Chenxing; Zhang, Yuzhi; Goodall, Rhys E. A.; Liang, Wenshuo; Singh, Anurag Kumar; Yao, Sikai; Zhang, Jingchao; Wentzcovitch, Renata; Han, Jiequn; Liu, Jie; Jia, Weile; York, Darrin M.; E, Weinan; Car, Roberto; Zhang, Linfeng; Wang, Han
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Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2023-05-01
err2
PREAI
errGiese, Timothy J.; York, Darrin M.
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Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology
errNUCLEIC ACIDS RESEARCH
IF13.1
err2023-04-18
err8
errOAAI
errMcCarthy, Erika; Ekesan, Soelen; Giese, Timothy J.; Wilson, Timothy J.; Deng, Jie; Huang, Lin; Lilley, David M. J.; York, Darrin M.
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Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2023-03-22
err18
errOAAI
errZeng, Jinzhe; Tao, Yujun; Giese, Timothy J.; York, Darrin M.
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errSave
Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2023-02-08
err0
errOAAI
errXu, Yuqing; Harris, Michael E.; York, Darrin M.; Wong, Kin-Yiu
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Research Directions

No research directions
Co-authors
Cooperation Journals
M
Martin Karplus
H-index: 167 · Papers: 981
B
Benoı̂t Roux
H-index: 128 · Papers: 722
C
Christopher J. Cramer
H-index: 110 · Papers: 864
R
Roberto Car
H-index: 108 · Papers: 589
A
Alexander D. MacKerell
H-index: 107 · Papers: 766
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