Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease. - Laurent David; Ray Luo 001; Michael K. Gilson (J. Comput. Chem., 2000)

Ligand-receptor docking with the Mining Minima optimizer. - Laurent David; Ray Luo 001; Michael K. Gilson (J. Comput. Aided Mol. Des., 2001)

Accelerated Poisson-Boltzmann calculations for static and dynamic systems. - Ray Luo 001; Laurent David; Michael K. Gilson (J. Comput. Chem., 2002)

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. - Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C. Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo 001; Tai-Sung Lee; James W. Caldwell; Junmei Wang; et al. (J. Comput. Chem., 2003)

The Amber biomolecular simulation programs. - David A. Case; Thomas E. Cheatham III; Tom Darden; Holger Gohlke; Ray Luo 001; Kenneth M. Merz Jr.; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J. Woods (J. Comput. Chem., 2005)

Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. - 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 001; Pierre Baldi; Rainer K. Brachmann; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Assessment of linear finite-difference Poisson-Boltzmann solvers. - Jun Wang 030; Ray Luo 001 (J. Comput. Chem., 2010)

Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation. - Wesley M. Botello-Smith; Ray Luo 001 (J. Chem. Inf. Model., 2015)

Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. - Wei Ye; Dingjue Ji; Wei Wang; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2015)

A semi-implicit augmented IIM for Navier-Stokes equations with open, traction, or free boundary conditions. - Zhilin Li 002; Li Xiao; Qin Cai; Hongkai Zhao; Ray Luo 001 (J. Comput. Phys., 2015)

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. - Changhao Wang; Peter H. Nguyen; Kevin Pham; Danielle Huynh; Thanh-Binh Nancy Le; Hongli Wang; Pengyu Y. Ren; Ray Luo 001 (J. Comput. Chem., 2016)

Synergistic Allosteric Mechanism of Fructose-1, 6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. - Jingxu Yang; Hao Liu 081; Xiaorui Liu; Chengbo Gu; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2016)

Numerical interpretation of molecular surface field in dielectric modeling of solvation. - Changhao Wang; Li Xiao; Ray Luo 001 (J. Comput. Chem., 2017)

The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. - Dong Song; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2017)

Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. - Wei Ye; Tianle Qian; Hao Liu 081; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2017)

Dynamical important residue network (DIRN): network inference via conformational change. - Quan Li; Ray Luo 001; Hai-Feng Chen (Bioinform., 2019)

An efficient second-order poisson-boltzmann method. - Haixin Wei; Ray Luo 001; Ruxi Qi (J. Comput. Chem., 2019)

Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. - D'artagnan Greene; Ruxi Qi; Remy Nguyen; Tianyin Qiu; Ray Luo 001 (J. Chem. Inf. Model., 2019)

Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units. - Ruxi Qi; Ray Luo 001 (J. Chem. Inf. Model., 2019)

Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. - Dong Song; Hao Liu 081; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2020)

Recent Force Field Strategies for Intrinsically Disordered Proteins. - Junxi Mu; Hao Liu 081; Jian Zhang 037; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2021)

Development of a Pantetheine Force Field Library for Molecular Modeling. - Shiji Zhao; Andrew J. Schaub; Shiou-Chuan Tsai; Ray Luo 001 (J. Chem. Inf. Model., 2021)

AmberTools. - 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; et al. (J. Chem. Inf. Model., 2023)

End-to-End Reaction Field Energy Modeling via Deep Learning based Voxel-to-voxel Transform. - Yongxian Wu; Qiang Zhu; Ray Luo 001 (CoRR, 2024)

Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials. - Yong Duan; Junmei Wang; Piotr Cieplak; Ray Luo 001 (J. Chem. Inf. Model., 2025)

Correction to "Development of a Pantetheine Force Field Library for Molecular Modeling". - Shiji Zhao; Andrew J. Schaub; Shiou-Chuan Tsai; Ray Luo 001 (J. Chem. Inf. Model., 2025)