Darrin M. York

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 11

Top Topics

Generalized Belief Propagation

Molecular Dynamics

Statistical Models

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

J. Comput. Aided Mol. Des.

Publications

Xinzijian Liu, Yanbo Han, Zhuoyuan Li, Jiahao Fan, Chengqian Zhang, Jinzhe Zeng, Yifan Shan, Yannan Yuan, Wei-Hong Xu, Yun-Pei Liu, Yuzhi Zhang, Tongqi Wen, Darrin M. York, Zhicheng Zhong, Hang Zheng, Jun Cheng, Linfeng Zhang, Han Wang
Dflow, a Python framework for constructing cloud-native AI-for-Science workflows. CoRR (2024)
David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri 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 M. 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 Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
AmberTools. J. Chem. Inf. Model. 63 (20) (2023)
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). J. Chem. Inf. Model. 62 (23) (2022)
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. J. Chem. Inf. Model. 61 (9) (2021)
Hsu-Chun Tsai, Yujun Tao, Tai-Sung Lee, Kenneth M. Merz Jr., Darrin M. York
Validation of Free Energy Methods in AMBER. J. Chem. Inf. Model. 60 (11) (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. J. Chem. Inf. Model. 60 (11) (2020)
Lin Frank Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.
Using AMBER18 for Relative Free Energy Calculations. J. Chem. Inf. Model. 59 (7) (2019)
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. J. Chem. Inf. Model. 58 (10) (2018)
Yuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, Darrin M. York, Zhuyan Guo
The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP. J. Comput. Aided Mol. Des. 30 (7) (2016)
Antons Treikalis, André Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. CoRR (2016)
Antons Treikalis, André Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. ICPP (2016)
Maria T. Panteva, George M. Giambasu, Darrin M. York
ion models commonly used in biomolecular simulations. J. Comput. Chem. 36 (13) (2015)
Ming Huang, Timothy J. Giese, Darrin M. York
Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models. J. Comput. Chem. 36 (18) (2015)
Kin-Yiu Wong, Yuqing Xu, Darrin M. York
path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. J. Comput. Chem. 35 (17) (2014)
Brian K. Radak, Tai-Sung Lee, Peng He, Melissa Romanus, Ole Weidner, Wei Dai, Emilio Gallicchio, Nan-Jie Deng, Darrin M. York, Ronald M. Levy, Shantenu Jha
A framework for flexible and scalable replica-exchange on production distributed CI. XSEDE (2013)
Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, V. Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30 (10) (2009)
Timothy J. Giese, Darrin M. York
Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities. J. Comput. Chem. 29 (12) (2008)
Evelyn Mayaan, Adam Moser, Alexander D. MacKerell Jr., Darrin M. York
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J. Comput. Chem. 28 (2) (2007)
Brent A. Gregersen, Darrin M. York
A charge-scaling implementation of the variational electrostatic projection method. J. Comput. Chem. 27 (1) (2006)
Edward C. Sherer, Darrin M. York, Christopher J. Cramer
Fast approximate methods for calculating nucleic acid base pair interaction energies. J. Comput. Chem. 24 (1) (2003)
Jana Khandogin, Anguang Hu, Darrin M. York
Electronic structure properties of solvated biomolecules: A quantum approach for macromolecular characterization. J. Comput. Chem. 21 (16) (2000)
Darrin M. York, Lee J. Bartolotti, Thomas A. Darden, Lee G. Pedersen, M. W. Anderson
Simulations of the Solution Structure of HIV-1 Protease in the Presence and Absence of Bound Zinc. J. Comput. Chem. 15 (1) (1994)