Ray Luo

26 papers Journal 26
YearRankTypeTitle / Venue / Authors
2025 J jnl
Correction to "Development of a Pantetheine Force Field Library for Molecular Modeling".
J. Chem. Inf. Model.
Shiji Zhao, Andrew J. Schaub, Shiou-Chuan Tsai, Ray Luo
2025 J jnl
Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials.
J. Chem. Inf. Model.
Yong Duan, Junmei Wang, Piotr Cieplak, Ray Luo
2024 J jnl
End-to-End Reaction Field Energy Modeling via Deep Learning based Voxel-to-voxel Transform.
CoRR
Yongxian Wu, Qiang Zhu, Ray Luo
2023 J jnl
AmberTools.
J. Chem. Inf. Model.
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.
2021 J jnl
Development of a Pantetheine Force Field Library for Molecular Modeling.
J. Chem. Inf. Model.
Shiji Zhao, Andrew J. Schaub, Shiou-Chuan Tsai, Ray Luo
2021 J jnl
Recent Force Field Strategies for Intrinsically Disordered Proteins.
J. Chem. Inf. Model.
Junxi Mu, Hao Liu, Jian Zhang, Ray Luo, Hai-Feng Chen
2020 J jnl
Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins.
J. Chem. Inf. Model.
Dong Song, Hao Liu, Ray Luo, Hai-Feng Chen
2019 J jnl
An efficient second-order poisson-boltzmann method.
J. Comput. Chem.
Haixin Wei, Ray Luo, Ruxi Qi
2019 J jnl
Dynamical important residue network (DIRN): network inference via conformational change.
Bioinform.
Quan Li, Ray Luo, Hai-Feng Chen
2019 J jnl
Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.
J. Chem. Inf. Model.
D'artagnan Greene, Ruxi Qi, Remy Nguyen, Tianyin Qiu, Ray Luo
2019 J jnl
Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units.
J. Chem. Inf. Model.
Ruxi Qi, Ray Luo
2017 J jnl
Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations.
J. Chem. Inf. Model.
Wei Ye, Tianle Qian, Hao Liu, Ray Luo, Hai-Feng Chen
2017 J jnl
Numerical interpretation of molecular surface field in dielectric modeling of solvation.
J. Comput. Chem.
Changhao Wang, Li Xiao, Ray Luo
2017 J jnl
The IDP-Specific Force Field
J. Chem. Inf. Model.
Dong Song, Ray Luo, Hai-Feng Chen
2016 J jnl
Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis.
J. Comput. Chem.
Changhao Wang, Peter H. Nguyen, Kevin Pham, Danielle Huynh, Thanh-Binh Nancy Le, Hongli Wang, Pengyu Y. Ren, Ray Luo
2016 J jnl
Synergistic Allosteric Mechanism of Fructose-1, 6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis.
J. Chem. Inf. Model.
Jingxu Yang, Hao Liu, Xiaorui Liu, Chengbo Gu, Ray Luo, Hai-Feng Chen
2015 J jnl
A semi-implicit augmented IIM for Navier-Stokes equations with open, traction, or free boundary conditions.
J. Comput. Phys.
Zhilin Li, Li Xiao, Qin Cai, Hongkai Zhao, Ray Luo
2015 J jnl
Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation.
J. Chem. Inf. Model.
Wesley M. Botello-Smith, Ray Luo
2015 J jnl
Test and Evaluation of
J. Chem. Inf. Model.
Wei Ye, Dingjue Ji, Wei Wang, Ray Luo, Hai-Feng Chen
2010 J jnl
Assessment of linear finite-difference Poisson-Boltzmann solvers.
J. Comput. Chem.
Jun Wang, Ray Luo
2006 J jnl
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants.
IEEE ACM Trans. Comput. Biol. Bioinform.
Samuel A. Danziger, Sanjay Joshua Swamidass, Jue Zeng, Lawrence R. Dearth, Qiang Lu, Jonathan H. Chen, Jianlin Cheng, Vinh P. Hoang, Hiroto Saigo, Ray Luo, Pierre Baldi, Rainer K. Brachmann, Richard H. Lathrop
2005 J jnl
The Amber biomolecular simulation programs.
J. Comput. Chem.
David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods
2003 J jnl
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
J. Comput. Chem.
Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Tai-Sung Lee, James W. Caldwell, Junmei Wang, Peter A. Kollman
2002 J jnl
Accelerated Poisson-Boltzmann calculations for static and dynamic systems.
J. Comput. Chem.
Ray Luo, Laurent David, Michael K. Gilson
2001 J jnl
Ligand-receptor docking with the Mining Minima optimizer.
J. Comput. Aided Mol. Des.
Laurent David, Ray Luo, Michael K. Gilson
2000 J jnl
Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease.
J. Comput. Chem.
Laurent David, Ray Luo, Michael K. Gilson