GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features
Lee, Tai-Sung, Cerutti, David S, Mermelstein, Dan, Lin, Charles, LeGrand, Scott, Giese, Timothy J, Roitberg, Adrian, Case, David A, Walker, Ross C, York, Darrin M
Published in Journal of chemical information and modeling (22.10.2018)
Published in Journal of chemical information and modeling (22.10.2018)
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Journal Article
A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method
Giese, Timothy J, York, Darrin M
Published in Journal of chemical theory and computation (13.03.2018)
Published in Journal of chemical theory and computation (13.03.2018)
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Journal Article
Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis
Giese, Timothy J, Ekesan, Şölen, York, Darrin M
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (20.05.2021)
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (20.05.2021)
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Journal Article
Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine–Thymine Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials
Tao, Yujun, Giese, Timothy J, York, Darrin M
Published in Molecules (Basel, Switzerland) (01.06.2024)
Published in Molecules (Basel, Switzerland) (01.06.2024)
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Journal Article
Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field
Giese, Timothy J, Huang, Ming, Chen, Haoyuan, York, Darrin M
Published in Accounts of chemical research (16.09.2014)
Published in Accounts of chemical research (16.09.2014)
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Journal Article
Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods
Huang, Ming, Giese, Timothy J, Lee, Tai-Sung, York, Darrin M
Published in Journal of chemical theory and computation (08.04.2014)
Published in Journal of chemical theory and computation (08.04.2014)
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Journal Article
Multipolar Ewald Methods, 1: Theory, Accuracy, and Performance
Giese, Timothy J, Panteva, Maria T, Chen, Haoyuan, York, Darrin M
Published in Journal of chemical theory and computation (10.02.2015)
Published in Journal of chemical theory and computation (10.02.2015)
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Journal Article
Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization
Kaminski, Steve, Giese, Timothy J, Gaus, Michael, York, Darrin M, Elstner, Marcus
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (13.09.2012)
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (13.09.2012)
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Journal Article
Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field
Giese, Timothy J, Panteva, Maria T, Chen, Haoyuan, York, Darrin M
Published in Journal of chemical theory and computation (10.02.2015)
Published in Journal of chemical theory and computation (10.02.2015)
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Journal Article
A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields
Giese, Timothy J, Chen, Haoyuan, Dissanayake, Thakshila, Giambaşu, George M, Heldenbrand, Hugh, Huang, Ming, Kuechler, Erich R, Lee, Tai-Sung, Panteva, Maria T, Radak, Brian K, York, Darrin M
Published in Journal of chemical theory and computation (12.03.2013)
Published in Journal of chemical theory and computation (12.03.2013)
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Journal Article
Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution
Zeng, Jinzhe, Giese, Timothy J, Ekesan, Şölen, York, Darrin M
Published in Journal of chemical theory and computation (09.11.2021)
Published in Journal of chemical theory and computation (09.11.2021)
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Journal Article
QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery
Zeng, Jinzhe, Tao, Yujun, Giese, Timothy J, York, Darrin M
Published in Journal of chemical theory and computation (28.02.2023)
Published in Journal of chemical theory and computation (28.02.2023)
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Journal Article
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery
Lee, Tai-Sung, Allen, Bryce K, Giese, Timothy J, Guo, Zhenyu, Li, Pengfei, Lin, Charles, McGee, T. Dwight, Pearlman, David A, Radak, Brian K, Tao, Yujun, Tsai, Hsu-Chun, Xu, Huafeng, Sherman, Woody, York, Darrin M
Published in Journal of chemical information and modeling (23.11.2020)
Published in Journal of chemical information and modeling (23.11.2020)
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Journal Article
Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states
Zeng, Jinzhe, Tao, Yujun, Giese, Timothy J, York, Darrin M
Published in The Journal of chemical physics (28.03.2023)
Published in The Journal of chemical physics (28.03.2023)
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