Darrin M York

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 69

Top Topics

Machine Learning

Helicobacter Pylori

Molecular Dynamics

Top Venues

Journal of chemical theory and computation

The journal of physical chemistry. B

Journal of chemical information and modeling

Journal of the American Chemical Society

This page only lists publications with an associated author ORCID identifier.

Publications

Yuxuan Wu, Shi Zhang, Darrin M York, Lu Wang
Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions. The journal of physical chemistry. B 128 (27) (2024)
Shi Zhang, Timothy J Giese, Tai-Sung Lee, Darrin M York
Alchemical Enhanced Sampling with Optimized Phase Space Overlap. Journal of chemical theory and computation (2024)
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York
Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of chemical theory and computation (2024)
Timothy J Giese, Jinzhe Zeng, Lauren Lerew, Erika McCarthy, Yujun Tao, Şölen Ekesan, Darrin M York
Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields. The journal of physical chemistry. B (2024)
Timothy J Giese, Jinzhe Zeng, Lauren Lerew, Erika McCarthy, Yujun Tao, Şölen Ekesan, Darrin M York
Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields. The journal of physical chemistry. B (2024)
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York
Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of chemical theory and computation 20 (5) (2024)
Yuxuan Wu, Shi Zhang, Darrin M York, Lu Wang
Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions. The journal of physical chemistry. B 128 (27) (2024)
Timothy J Giese, Jinzhe Zeng, Lauren Lerew, Erika McCarthy, Yujun Tao, Şölen Ekesan, Darrin M York
Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields. The journal of physical chemistry. B 128 (26) (2024)
Yujun Tao, Timothy J Giese, Darrin M York
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. Molecules (Basel, Switzerland) 29 (11) (2024)
Shi Zhang, Timothy J Giese, Tai-Sung Lee, Darrin M York
Alchemical Enhanced Sampling with Optimized Phase Space Overlap. Journal of chemical theory and computation 20 (9) (2024)
Hsu-Chun Tsai, James Xu, Zhenyu Guo, Yinhui Yi, Chuan Tian, Xinyu Que, Timothy J Giese, Tai-Sung Lee, Darrin M York, Abir Ganguly, Albert Pan
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach. Journal of chemical information and modeling (2024)
Yujun Tao, Timothy J Giese, Darrin M York
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. Molecules (Basel, Switzerland) 29 (11) (2024)
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York
Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of chemical theory and computation 20 (5) (2024)
Yujun Tao, Timothy J Giese, Darrin M York
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. Molecules (Basel, Switzerland) 29 (11) (2024)
Timothy J Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M York
Surface-Accelerated String Method for Locating Minimum Free Energy Paths. Journal of chemical theory and computation 20 (5) (2024)
Shi Zhang, Timothy J Giese, Tai-Sung Lee, Darrin M York
Alchemical Enhanced Sampling with Optimized Phase Space Overlap. Journal of chemical theory and computation 20 (9) (2024)
Yuxuan Wu, Shi Zhang, Darrin M York, Lu Wang
Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions. The journal of physical chemistry. B (2024)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society 145 (5) (2023)
Darrin M York
Modern Alchemical Free Energy Methods for Drug Discovery Explained. ACS physical chemistry Au 3 (6) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation 19 (4) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states. The Journal of chemical physics 158 (12) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation 19 (4) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation 19 (4) (2023)
Yuqing Xu, Michael E Harris, Darrin M York, Kin-Yiu Wong
Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models. Journal of chemical theory and computation 19 (4) (2023)
Timothy J Giese, Darrin M York
Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations. The Journal of chemical physics 158 (17) (2023)
Tai-Sung Lee, Hsu-Chun Tsai, Abir Ganguly, Darrin M York
ACES: Optimized Alchemically Enhanced Sampling. Journal of chemical theory and computation (2023)
Yuqing Xu, Michael E Harris, Darrin M York, Kin-Yiu Wong
Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models. Journal of chemical theory and computation 19 (4) (2023)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society 145 (5) (2023)
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, Gerardo Andrés Cisneros, Vinícius Wilian D Cruzeiro, Negin Forouzesh, Timothy J Giese, Andreas W Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet C 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 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 L Simmerling, Darrin M York, Maria C Nagan, Kenneth M Merz
AmberTools. Journal of chemical information and modeling (2023)
Timothy J Giese, Darrin M York
Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations. The Journal of chemical physics 158 (17) (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation 19 (4) (2023)
Suhyun Yoon, Edward Ollie, Darrin M York, Joseph A Piccirilli, Michael E Harris
Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis. Biochemistry (2023)
Timothy J Giese, Darrin M York
Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations. The Journal of chemical physics 158 (17) (2023)
Erika McCarthy, Şölen Ekesan, Timothy J Giese, Timothy J Wilson, Jie Deng, Lin Huang, David M J Lilley, Darrin M York
Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology. Nucleic acids research (2023)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society 145 (5) (2023)
Hsu-Chun Tsai, Tai-Sung Lee, Abir Ganguly, Timothy J Giese, Maximilian Ccjc Ebert, Paul Labute, Kenneth M Merz, Darrin M York
AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways. Journal of chemical theory and computation (2023)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society (2023)
Yuqing Xu, Michael E Harris, Darrin M York, Kin-Yiu Wong
Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models. Journal of chemical theory and computation (2023)
Jinzhe Zeng, Yujun Tao, Timothy J Giese, Darrin M York
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery. Journal of chemical theory and computation (2023)
Benjamin P Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J Giese, Erika McCarthy, Michael E Harris, Darrin M York, Joseph A Piccirilli
Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. Journal of the American Chemical Society 145 (5) (2023)
Şölen Ekesan, Erika McCarthy, David A Case, Darrin M York
RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis. The journal of physical chemistry. B 126 (32) (2022)
Tushar Aggarwal, William A Hansen, Jonathan Hong, Abir Ganguly, Darrin M York, Sagar D Khare, Enver Cagri Izgu
Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign. ACS chemical biology 17 (7) (2022)
Timothy J Giese, Jinzhe Zeng, Şölen Ekesan, Darrin M York
Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions. Journal of chemical theory and computation 18 (7) (2022)
Timothy J Giese, Jinzhe Zeng, Darrin M York
Multireference Generalization of the Weighted Thermodynamic Perturbation Method. The journal of physical chemistry. A 126 (45) (2022)
Şölen Ekesan, Darrin M York
Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme. Organic & biomolecular chemistry 20 (31) (2022)
Abir Ganguly, Hsu-Chun Tsai, Mario Fernández-Pendás, Tai-Sung Lee, Timothy J Giese, Darrin M York
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA). Journal of chemical information and modeling (2022)
Timothy J Giese, Şölen Ekesan, Darrin M York
Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis. The journal of physical chemistry. A 125 (19) (2021)
Han Zhang, Seonghoon Kim, Timothy J Giese, Tai-Sung Lee, Jumin Lee, Darrin M York, Wonpil Im
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER. Journal of chemical information and modeling 61 (9) (2021)
Estella F Yee, Sabine Oldemeyer, Elena Böhm, Abir Ganguly, Darrin M York, Tilman Kottke, Brian R Crane
Peripheral Methionine Residues Impact Flavin Photoreduction and Protonation in an Engineered LOV Domain Light Sensor. Biochemistry 60 (15) (2021)
Timothy J Giese, Darrin M York
Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints. Journal of chemical theory and computation 17 (3) (2021)
Jinzhe Zeng, Timothy J Giese, Şölen Ekesan, Darrin M York
Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution. Journal of chemical theory and computation 17 (11) (2021)
Tai-Sung Lee, Zhixiong Lin, Bryce K Allen, Charles Lin, Brian K Radak, Yujun Tao, Hsu-Chun Tsai, Woody Sherman, Darrin M York
Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials. Journal of chemical theory and computation 16 (9) (2020)
Tai-Sung Lee, Bryce K Allen, Timothy J Giese, Zhenyu Guo, Pengfei Li, Charles Lin, T Dwight McGee, David A Pearlman, Brian K Radak, Yujun Tao, Hsu-Chun Tsai, Huafeng Xu, Woody Sherman, Darrin M York
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. Journal of chemical information and modeling 60 (11) (2020)
Abir Ganguly, Benjamin P Weissman, Timothy J Giese, Nan-Sheng Li, Shuichi Hoshika, Saieesh Rao, Steven A Benner, Joseph A Piccirilli, Darrin M York
Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme. Nature chemistry 12 (2) (2020)
Hsu-Chun Tsai, Yujun Tao, Tai-Sung Lee, Kenneth M Merz, Darrin M York
Validation of Free Energy Methods in AMBER. Journal of chemical information and modeling 60 (11) (2020)
Timothy J Giese, Darrin M York
Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods. Journal of chemical theory and computation 15 (10) (2019)
Philip C Bevilacqua, Michael E Harris, Joseph A Piccirilli, Colin S Gaines, Abir Ganguly, Ken Kostenbader, Şölen Ekesan, Darrin M York
An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes. ACS chemical biology 14 (6) (2019)
George M Giambaşu, David A Case, Darrin M York
Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory. Journal of the American Chemical Society 141 (6) (2019)
Xiao Li, Darrin M York, Matthew P Meyer
Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction. The journal of physical chemistry. A 123 (17) (2019)
Lin Frank Song, Tai-Sung Lee, Jin-Xia Liang, Darrin M York, Kenneth M Merz
Using AMBER18 for Relative Free Energy Calculations. Journal of chemical information and modeling 59 (7) (2019)
Ken Kostenbader, Darrin M York
Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme. RNA (New York, N.Y.) 25 (11) (2019)
Colin S Gaines, Joseph A Piccirilli, Darrin M York
The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design. RNA (New York, N.Y.) 26 (2) (2019)
Şölen Ekesan, Darrin M York
Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation. The journal of physical chemistry. B 123 (22) (2019)
Timothy J Giese, Darrin M York
A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method. Journal of chemical theory and computation 14 (3) (2018)
Tai-Sung Lee, David S Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J Giese, Adrian E Roitberg, David A Case, Ross C Walker, Darrin M York
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. Journal of chemical information and modeling 58 (10) (2018)
Haoyuan Chen, Timothy J Giese, Barbara L Golden, Darrin M York
Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations. Biochemistry 56 (24) (2017)
Ming Huang, Thakshila Dissanayake, Erich Kuechler, Brian K Radak, Tai-Sung Lee, Timothy J Giese, Darrin M York
A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations. Journal of chemical theory and computation 13 (9) (2017)
Colin S Gaines, Darrin M York
Model for the Functional Active State of the TS Ribozyme from Molecular Simulation. Angewandte Chemie (International ed. in English) 56 (43) (2017)
Tai-Sung Lee, Yuan Hu, Bradley S Sherborne, Zhuyan Guo, Darrin M York
Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration. Journal of chemical theory and computation 13 (7) (2017)