Publications

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Zhen Huang, Ray Luo, Yong Duan (2026). A Density-Consistent, Finite van der Waals Potential from Gaussian Atomic Densities. The Journal of Physical Chemistry Letters.

Yongxian Wu, Piotr Cieplak, Yong Duan, Ray Luo (2026). pGM5P-26: A Polarizable Gaussian Multipole Water Model with Transferable Temperature-Dependent Thermodynamics. Journal of Chemical Theory and Computation.

Piotr Cieplak, Ray Luo, Yong Duan (2026). Charge Transfer Interactions in Quantum Mechanics and in Classical Force Fields. The Journal of Physical Chemistry B.

Jeongmin An, Zhen Huang, Amrutha Kizhedathu, Tian Lan, Tzuling Lin, Hyejin Joo, Eshan Malinda Thilakaratne, Yuhan Liu, Yun Yi Xu, Bing Yang, Pablo Lara-Gonzalez, Rahul Warrior, Ray Luo, Wenqi Wang (2026). STK38/L promote tissue growth and cancer by inhibiting the Hippo pathway. Genes & Development.

Yongxian Wu, Qiankang Wang, Robin Jiang, Ray Luo (2026). AmberTorchPB: A Unified Framework for Poisson–Boltzmann-Based Reaction Field Energy Calculation via Tensor Computation. Journal of Chemical Theory and Computation.

Tzuling Lin, Zhen Huang, Ray Luo (2026). BPS2026 – Methodological considerations for MM-PBSA calculations of binding affinities in highly charged protein-protein systems: A systematic study. Biophysical Journal.

Zhen Huang, Yong Duan, Xiongwu Wu, Ray Luo (2025). DEGAUSS: A Novel Softcore Force Field Using Double Exponential van der Waals and Gaussian Charge for Molecular Dynamics Simulations I: Theory and Validation. Journal of Chemical Theory and Computation.

Taoyu Niu, Junmei Wang, Zhen Huang, Ray Luo, Piotr Cieplak, Yong Duan (2025). Optimization of Lennard–Jones Parameters for Induced Dipole Polarizable Gaussian Multipole Force Field. The Journal of Physical Chemistry B.

Yongxian Wu, Qiang Zhu, Ray Luo (2025). End-to-End Modeling of Reaction Field Energy Using Data-Driven Geometric Graph Neural Networks. Journal of Chemical Theory and Computation.

Yongxian Wu, Ray Luo (2025). Grid-Context Convolutional Model for Efficient Molecular Surface Construction from Point Clouds. Journal of Chemical Theory and Computation.

Zhen Huang, Xiongwu Wu, Ray Luo (2025). Isotropic Periodic Sum for Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

Yongxian Wu, Qiang Zhu, Zhen Huang, Piotr Cieplak, Yong Duan, Ray Luo (2025). Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization. Journal of Chemical Theory and Computation.

Yong Duan, Junmei Wang, Piotr Cieplak, Ray Luo (2025). Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials. Journal of Chemical Information and Modeling.

Zhen Huang, Yongxian Wu, Yong Duan, Ray Luo (2025). Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation.

Ray Luo (2025). Role of artificial intelligence in revolutionizing drug discovery. Fundamental Research.

Ray Luo (2025). Modeling Molecular Recognition with the Polarizable Gaussian Multipole Model. SMT.

Cizhang Zhao, Tianhong Wang, Ray Luo (2025). Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R.

Yong Duan, Taoyu Niu, Junmei Wang, Piotr Cieplak, Ray Luo (2024). PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents. Journal of Chemical Theory and Computation.

Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2024). Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

Qiang Zhu, Yongxian Wu, Ray Luo (2024). Understanding and fine-tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine. Biophysical Journal.

Ashfaq Ur Rehman, Cizhang Zhao, Yongxian Wu, Qiang Zhu, Ray Luo (2024). Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy. International Journal of Molecular Sciences.

Derek Aspacio, Yulai Zhang, Youtian Cui, Emma Luu, Edward King, William B. Black, Sean Perea, Qiang Zhu, Yongxian Wu, Ray Luo, Justin B. Siegel, Han Li (2024). Shifting redox reaction equilibria on demand using an orthogonal redox cofactor. Nature Chemical Biology.

Hossain Shadman, Jesse D. Ziebarth, Caleb E. Gallops, Ray Luo, Zhengxin Li, Hai-Feng Chen, Yongmei Wang (2024). Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities. Biophysical Journal.

Yongxian Wu, Qiang Zhu, Ray Luo (2024). Many-body effects in machine-learned molecular surface predictions. Biophysical Journal.

Ray Luo (2024). End-to-end reaction field energy modeling via deep learning based voxel-to-voxel transform. arXiv preprint arXiv:.

Yongxian Wu, Haixin Wei, Qiang Zhu, Ray Luo (2023). Grid-Robust Efficient Neural Interface Model for Universal Molecule Surface Construction from Point Clouds. The Journal of Physical Chemistry Letters.

Qiang Zhu, Yongxian Wu, Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2023). Streamlining and Optimizing Strategies of Electrostatic Parameterization. Journal of Chemical Theory and Computation.

Zhen Huang, Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo, Haixin Wei (2023). Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models. Journal of Chemical Theory and Computation.

Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2023). Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

Hongchao Ji, Xue Lu, Shiji Zhao, Qiqi Wang, Bin Liao, Ludwig G. Bauer, Kilian v. M. Huber, Ray Luo, Ruijun Tian, Chris Soon Heng Tan (2023). Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions. Cell Chemical Biology.

Qiang Zhu, Ray Luo (2023). Recent Advances in Biomolecular Recognition. International Journal of Molecular Sciences.

Noor Ul Ain Nazir, Muhammad Haroon Shaukat, Ray Luo, Shah Rukh Abbas (2023). Novel breath biomarkers identification for early detection of hepatocellular carcinoma and cirrhosis using ML tools and GCMS. PLOS ONE.

Ray Luo (2023). Computational approaches for the design of modulators targeting protein-protein interactions. Expert opinion on drug discovery.

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). PyRESP : A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields. Journal of Chemical Theory and Computation.

Beenish Khurshid, Ashfaq Ur Rehman, Ray Luo, Alamzeb Khan, Abdul Wadood, Jamshed Anwar (2022). Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations. ACS Omega.

Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). Stress tensor and constant pressure simulation for polarizable Gaussian multipole model. The Journal of Chemical Physics.

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). PyRESP: A flexible program for polarizable force field parameterizations. Biophysical Journal.

Edward King, Sarah Maxel, Yulai Zhang, Karissa C. Kenney, Youtian Cui, Emma Luu, Justin B. Siegel, Gregory A. Weiss, Ray Luo, Han Li (2022). Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nature Communications.

Xiong Chen, Shanping Ji, Zheyi Liu, Xiao Yuan, Congsheng Xu, Ruxi Qi, An He, Heng Zhao, Haiping Song, Chunlei Xiao, Weina Gao, Peng R. Chen, Ray Luo, Pengfei Li, Fangjun Wang, Xueming Yang, Ruijun Tian (2022). Motif-dependent immune co-receptor interactome profiling by photoaffinity chemical proteomics. Cell Chemical Biology.

Hongchao Ji, Xue Lu, Shiji Zhao, Qiqi Wang, Liao Bin, Kilian v. M. Huber, Ray Luo, Ruijun Tian, Chris Soon Heng Tan (2022). Matrix-Augmented Pooling Strategy for High-Throughput Target Deconvolution Reveals Cell Type Specific Off-Targets and Responses. SSRN Electronic Journal.

Edward King, Youtian Cui, Derek Aspacio, Frances Nicklen, Linyue Zhang, Sarah Maxel, Ray Luo, Justin B. Siegel, Erick Aitchison, Han Li (2022). Engineering Embden–Meyerhof–Parnas Glycolysis to Generate Noncanonical Reducing Power. ACS Catalysis.

Linyue Zhang, Edward King, William B. Black, Christian M. Heckmann, Allison Wolder, Youtian Cui, Francis Nicklen, Justin B. Siegel, Ray Luo, Caroline E. Paul, Han Li (2022). Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nature Communications.

Ray Luo (2022). Development of polarizable Gaussian multipole model. Biophysical Journal.

Haixin Wei, Zekai Zhao, Ray Luo (2022). Advancing MM/PBSA calculations with machine learning and cuda GPUs. Biophysical Journal.

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

Haixin Wei, Zekai Zhao, Ray Luo (2021). Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations. Journal of Chemical Theory and Computation.

Sarah Maxel, Samer Saleh, Edward King, Derek Aspacio, Linyue Zhang, Ray Luo, Han Li (2021). Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst. ACS Synthetic Biology.

Edward King, Ruxi Qi, Han Li, Ray Luo, Erick Aitchison (2021). Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. Journal of Chemical Theory and Computation.

Shiji Zhao, Andrew J. Schaub, Shiou-Chuan Tsai, Ray Luo (2021). Development of a Pantetheine Force Field Library for Molecular Modeling. Journal of Chemical Information and Modeling.

Ray Luo (2021). Recent force field strategies for intrinsically disordered proteins. Journal of chemical information and modeling.

Edward King, Erick Aitchison, Han Li, Ray Luo (2021). Recent Developments in Free Energy Calculations for Drug Discovery. Frontiers in Molecular Biosciences.

Sarah Maxel, Edward King, Yulai Zhang, Ray Luo, Han Li (2020). Leveraging Oxidative Stress to Regulate Redox Balance-Based, In Vivo Growth Selections for Oxygenase Engineering. ACS Synthetic Biology.

Dong Song, Hao Liu, Ray Luo, Hai-Feng Chen (2020). Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. Journal of Chemical Information and Modeling.

Shiji Zhao, Fanglue Ni, Tianyin Qiu, Jacob Wolff, Shiou-Chuan Tsai, Ray Luo (2020). Molecular Basis for Polyketide Ketoreductase–Substrate Interactions. International Journal of Molecular Sciences.

Sarah Maxel, Linyue Zhang, Edward King, Ana Paula Acosta, Ray Luo, Han Li (2020). In Vivo, High-Throughput Selection of Thermostable Cyclohexanone Monooxygenase (CHMO). Catalysts.

Haixin Wei, Ruxi Qi, Junmei Wang, Piotr Cieplak, Yong Duan, Ray Luo (2020). Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations. The Journal of Chemical Physics.

Han Han, Wenqi Wang (2020). Abstract A24: Functional annotation of the Hippo somatic mutations in human cancer. Molecular Cancer Research.

Song-Bo Lu, Hongxin Chai, Jas S. Ward, Mao Quan, Jin Zhang, Kari Rissanen, Ray Luo, Liu-Pan Yang, Wei Jiang (2020). A 2,3-dialkoxynaphthalene-based naphthocage. Chemical Communications.

Yangpeng Zhang, Hao Liu, Sheng Yang, Ray Luo, Hai-Feng Chen (2019). Well-Balanced Force Field ff03CMAP for Folded and Disordered Proteins. Journal of Chemical Theory and Computation.

Junmei Wang, Piotr Cieplak, Ray Luo, Yong Duan (2019). Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy. Journal of Chemical Theory and Computation.

Ray Luo (2019). Polarizable Gaussian Multipole Framework for Electrostatic Interactions in Biomolecules. APS March Meeting Abstracts.

Ray Luo (2019). Molecular basis for interactions between an acyl carrier protein and a ketosynthase. Nature chemical biology.

Haixin Wei, Aaron Luo, Tianyin Qiu, Ray Luo, Ruxi Qi (2019). Improved Poisson–Boltzmann Methods for High-Performance Computing. Journal of Chemical Theory and Computation.

D’Artagnan Greene, Ruxi Qi, Remy Nguyen, Tianyin Qiu, Ray Luo (2019). Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. Journal of Chemical Information and Modeling.

Hao Liu, Dong Song, Yangpeng Zhang, Sheng Yang, Ray Luo, Hai-Feng Chen (2019). Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins. Physical Chemistry Chemical Physics.

Rebecca E Vargas, Vy Thuy Duong, Han Han, Albert Paul Ta, Yuxuan Chen, Shiji Zhao, Bing Yang, Gayoung Seo, Kimberly Chuc, Sunwoo Oh, Amal El Ali, Olga v Razorenova, Junjie Chen, Ray Luo, Xu Li, Wenqi Wang (2019). Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor. The EMBO Journal.

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

Andrew J. Schaub, Gabriel O. Moreno, Shiji Zhao, Hau v. Truong, Ray Luo, Shiou-Chuan Tsai (2019). Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases. Methods in Enzymology.

Haixin Wei, Ray Luo, Ruxi Qi (2019). An efficient second‐order poisson–boltzmann method. Journal of Computational Chemistry.

William B. Black, Edward King, Yixi Wang, Ana Jenic, Andrew T. Rowley, Kosuke Seki, Ray Luo, Han Li (2018). Engineering a Coenzyme A Detour To Expand the Product Scope and Enhance the Selectivity of the Ehrlich Pathway. ACS Synthetic Biology.

Vy T. Duong, Zihao Chen, Mahendra T. Thapa, Ray Luo (2018). Computational Studies of Intrinsically Disordered Proteins. The Journal of Physical Chemistry B.

Linyue Zhang, Edward King, Ray Luo, Han Li (2018). Development of a High-Throughput, In Vivo Selection Platform for NADPH-Dependent Reactions Based on Redox Balance Principles. ACS Synthetic Biology.

Bryan D. Ellis, Jacob C. Milligan, Alexander R. White, Vy Duong, Pilar X. Altman, Lina Y. Mohammed, Matthew P. Crump, John Crosby, Ray Luo, Christopher D. Vanderwal, Shiou-Chuan Tsai (2018). An Oxetane-Based Polyketide Surrogate To Probe Substrate Binding in a Polyketide Synthase. Journal of the American Chemical Society.

D’Artagnan Greene, Theodora Po, Jennifer Pan, Tanya Tabibian, Ray Luo (2018). Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies. The Journal of Physical Chemistry B.

Ruxi Qi, Ray Luo (2018). Robustness and Efficiency of Poisson–Boltzmann Modeling on Graphics Processing Units. Journal of Chemical Information and Modeling.

Han Han, Ruxi Qi, Jeff Jiajing Zhou, Albert Paul Ta, Bing Yang, Hiroki J. Nakaoka, Gayoung Seo, Kun-Liang Guan, Ray Luo, Wenqi Wang (2018). Regulation of the Hippo Pathway by Phosphatidic Acid-Mediated Lipid-Protein Interaction. Molecular Cell.

Changhao Wang, D'Artagnan Greene, Li Xiao, Ruxi Qi, Ray Luo (2018). Recent Developments and Applications of the MMPBSA Method. Frontiers in Molecular Biosciences.

Hao Liu, Xiang Guo, Jingcheng Han, Ray Luo, Hai-Feng Chen (2018). Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB. The Journal of Chemical Physics.

Ray Luo (2018). Methods Supporting Information. Biophysical Journal,.

Hao Liu, Dong Song, Hui Lu, Ray Luo, Hai‐Feng Chen (2018). Intrinsically disordered protein‐specific force field <scp>CHARMM</scp>36<scp>IDPSFF</scp>. Chemical Biology & Drug Design.

Vy T. Duong, Mahendra Thapa, Ray Luo (2018). Improved Accuracy and Convergence of Intrinsically Disordered Protein Molecular Dynamics Simulations Using the ff14IDPSFF Force Field. Biophysical Journal.

Changhao Wang, Pengyu Ren, Ray Luo (2017). Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling. The Journal of Physical Chemistry B.

Dong Song, Ray Luo, Hai-Feng Chen (2017). The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling.

Wei Ye, Tianle Qian, Hao Liu, Ray Luo, Hai-Feng Chen (2017). Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. Journal of Chemical Information and Modeling.

Changhao Wang, Li Xiao, Ray Luo (2017). Numerical interpretation of molecular surface field in dielectric modeling of solvation. Journal of Computational Chemistry.

Li Xiao, Ray Luo (2017). Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid. The Journal of Chemical Physics.

Tianle Qian, Jing Wo, Yan Zhang, Quanwei Song, Guoqiang Feng, Ray Luo, Shuangjin Lin, Geng Wu, Hai-Feng Chen (2017). Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode. Scientific Reports.

Xiang Guo, Jincheng Han, Ray Luo, Hai-Feng Chen (2017). Correction: Conformation dynamics of the intrinsically disordered protein c-Myb with the ff99IDPs force field. RSC Advances.

Ruxi Qi, Wesley M. Botello-Smith, Ray Luo (2017). Acceleration of Linear Finite-Difference Poisson–Boltzmann Methods on Graphics Processing Units. Journal of Chemical Theory and Computation.

Li Xiao, Jianxiong Diao, D’Artagnan Greene, Junmei Wang, Ray Luo (2017). A Continuum Poisson–Boltzmann Model for Membrane Channel Proteins. Journal of Chemical Theory and Computation.

D’Artagnan Greene, Wesley M. Botello-Smith, Alec Follmer, Li Xiao, Eleftherios Lambros, Ray Luo (2016). Modeling Membrane Protein–Ligand Binding Interactions: The Human Purinergic Platelet Receptor. The Journal of Physical Chemistry B.

Jingxu Yang, Hao Liu, Xiaorui Liu, Chengbo Gu, Ray Luo, Hai-Feng Chen (2016). Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. Journal of Chemical Information and Modeling.

Jinmai Zhang, Huajie Luo, Hao Liu, Wei Ye, Ray Luo, Hai-Feng Chen (2016). Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Scientific Reports.

Wei Wang, Cheng Jiang, Jinmai Zhang, Wei Ye, Ray Luo, Hai-Feng Chen (2016). Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Scientific Reports.

Li Xiao, Changhao Wang, Xiang Ye, Ray Luo (2016). Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions. The Journal of Physical Chemistry B.

Changhao Wang, Peter H. Nguyen, Kevin Pham, Danielle Huynh, Thanh‐Binh Nancy Le, Hongli Wang, Pengyu Ren, Ray Luo (2016). Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis. Journal of Computational Chemistry.

Jin-Mai Zhang, Cheng Jiang, Wei Ye, Ray Luo, Hai-Feng Chen (2016). Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network. Molecular BioSystems.

Dong Song, Wei Wang, Wei Ye, Dingjue Ji, Ray Luo, Hai‐Feng Chen (2016). <i>ff14IDPs</i> force field improving the conformation sampling of intrinsically disordered proteins. Chemical Biology & Drug Design.

Wei Ye, Dingjue Ji, Wei Wang, Ray Luo, Hai-Feng Chen (2015). Test and Evaluation of <i>ff99IDPs</i> Force Field for Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling.

David R. Jackson, Stephanie S. Tu, MyChi Nguyen, Jesus F. Barajas, Andrew J. Schaub, Daniel Krug, Dominik Pistorius, Ray Luo, Rolf Müller, Shiou-Chuan Tsai (2015). Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis. ACS Chemical Biology.

Lishi Xu, Wei Ye, Cheng Jiang, Jingxu Yang, Jinmai Zhang, Yan Feng, Ray Luo, Hai-Feng Chen (2015). Recognition Mechanism between Lac Repressor and DNA with Correlation Network Analysis. The Journal of Physical Chemistry B.

Jesus F. Barajas, Ryan M. Phelan, Andrew J. Schaub, Jaclyn T. Kliewer, Peter J. Kelly, David R. Jackson, Ray Luo, Jay D. Keasling, Shiou-Chuan Tsai (2015). Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols. Chemistry & Biology.

Wesley M. Botello-Smith, Ray Luo (2015). Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson–Boltzmann Equation. Journal of Chemical Information and Modeling.

Zhilin Li, Li Xiao, Qin Cai, Hongkai Zhao, Ray Luo (2015). A semi-implicit augmented IIM for Navier–Stokes equations with open, traction, or free boundary conditions. Journal of Computational Physics.

Ray Luo (2014). New force field on modeling intrinsically disordered proteins. Chemical biology & drug design.

Ray Luo (2014). Molecular Dynamic Studies of the Reductase Domain of Polyketide Synthase from the Myxobacterium Stigmatella Aurantiaca. PROTEIN SCIENCE.

Ray Luo (2014). Electrostatics and polarization effects in biophysical chemistry: in silico and in vitro. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY.

Wesley M. Botello-Smith, Xingping Liu, Qin Cai, Zhilin Li, Hongkai Zhao, Ray Luo (2013). Numerical Poisson–Boltzmann model for continuum membrane systems. Chemical Physics Letters.

Changhao Wang, Jun Wang, Qin Cai, Zhilin Li, Hong-Kai Zhao, Ray Luo (2013). Exploring accurate Poisson–Boltzmann methods for biomolecular simulations. Computational and Theoretical Chemistry.

Xingping Liu, Changhao Wang, Jun Wang, Zhilin Li, Hongkai Zhao, Ray Luo (2013). Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications. Phys. Chem. Chem. Phys..

Li Xiao, Qin Cai, Xiang Ye, Jun Wang, Ray Luo (2013). Electrostatic forces in the Poisson-Boltzmann systems. The Journal of Chemical Physics.

Wei Wang, Wei Ye, Qingfen Yu, Cheng Jiang, Jian Zhang, Ray Luo, Hai-Feng Chen (2013). Conformational Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study. The Journal of Physical Chemistry B.

Jun Wang, Qin Cai, Ye Xiang, Ray Luo (2012). Reducing Grid Dependence in Finite-Difference Poisson–Boltzmann Calculations. Journal of Chemical Theory and Computation.

Qin Cai, Jun Wang, Meng-Juei Hsieh, Xiang Ye, Ray Luo (2012). Poisson–Boltzmann Implicit Solvation Models. Annual Reports in Computational Chemistry.

Qin Cai, Xiang Ye, Ray Luo (2012). Dielectric pressure in continuum electrostatic solvation of biomolecules. Physical Chemistry Chemical Physics.

Junmei Wang, Piotr Cieplak, Jie Li, Qin Cai, Meng-Juei Hsieh, Ray Luo, Yong Duan (2012). Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization. The Journal of Physical Chemistry B.

Wei Ye, Fang Qin, Jian Zhang, Ray Luo, Hai-Feng Chen (2012). Atomistic Mechanism of MicroRNA Translation Upregulation via Molecular Dynamics Simulations. PLoS ONE.

Ray Luo (2011). Virtual screening using molecular simulations. Proteins: Structure, Function, and Bioinformatics.

Ray Luo (2011). This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. AMBER.

Qin Cai, Xiang Ye, Jun Wang, Ray Luo (2011). On-the-Fly Numerical Surface Integration for Finite-Difference Poisson–Boltzmann Methods. Journal of Chemical Theory and Computation.

Qin Cai, Xiang Ye, Jun Wang, Ray Luo (2011). Dielectric boundary force in numerical Poisson–Boltzmann methods: Theory and numerical strategies. Chemical Physics Letters.

Ray Luo (2011). Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability. The journal of physical chemistry B.

Ray Luo (2011). Annual Reports in Computational Chemistry. Annual Reports in Computational Chemistry.

C. -Z. Li, M. Koter, X. Ye, S. -F. Zhou, W. Chou, R. Luo, P. D. Gershon (2010). Widespread but Small-Scale Changes in the Structural and Dynamic Properties of Vaccinia Virus Poly(A) Polymerase upon Association with Its Processivity Factor in Solution. Biochemistry.

Jun Wang, Chunhu Tan, Emmanuel Chanco, Ray Luo (2010). Quantitative analysis of Poisson–Boltzmann implicit solvent in molecular dynamics. Phys. Chem. Chem. Phys..

Meng-Juei Hsieh, Ray Luo (2010). Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations. Journal of Molecular Modeling.

Meng-Juei Hsieh, Ray Luo (2010). Balancing Simulation Accuracy and Efficiency with the Amber United Atom Force Field. The Journal of Physical Chemistry B.

Jun Wang, Ray Luo (2010). Assessment of linear finite‐difference Poisson–Boltzmann solvers. Journal of Computational Chemistry.

Ray Luo (2010). AMBER11. University of California, San Francisco. There is no corresponding record for this reference,.

Xiang Ye, Jun Wang, Ray Luo (2010). A Revised Density Function for Molecular Surface Calculation in Continuum Solvent Models. Journal of Chemical Theory and Computation.

Yuhong Tan, Ray Luo (2009). Structural and functional implications of p53 missense cancer mutations. PMC Biophysics.

Xiang Ye, Qin Cai, Wei Yang, Ray Luo (2009). Roles of Boundary Conditions in DNA Simulations: Analysis of Ion Distributions with the Finite-Difference Poisson-Boltzmann Method. Biophysical Journal.

Qin Cai, Meng-Juei Hsieh, Jun Wang, Ray Luo (2009). Performance of Nonlinear Finite-Difference Poisson−Boltzmann Solvers. Journal of Chemical Theory and Computation.

Qin Cai, Jun Wang, Hong-Kai Zhao, Ray Luo (2009). On removal of charge singularity in Poisson–Boltzmann equation. The Journal of Chemical Physics.

Yu-Hong Tan, Y. Morris Chen, Xiang Ye, Qiang Lu, Vira Tretyachenko-Ladokhina, Wei Yang, Donald F. Senear, Ray Luo (2009). Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations. Biophysical Chemistry.

Jun Wang, Qin Cai, Zhi-Lin Li, Hong-Kai Zhao, Ray Luo (2009). Achieving energy conservation in Poisson–Boltzmann molecular dynamics: Accuracy and precision with finite-difference algorithms. Chemical Physics Letters.

Yu-Hong Tan, Ray Luo (2008). Protein Stability Prediction: A Poisson−Boltzmann Approach. The Journal of Physical Chemistry B.

Jun Wang, Chunhu Tan, Yu-Hong Tan, Qiang Lu, Ray Luo (2008). Poisson-Boltzmann Solvents in Molecular Dynamics Simulations. Communications in Computational Physics.

Tyler Paz Korman, Yu-Hong Tan, Justin Wong, Ray Luo, Shiou-Chuan Tsai (2008). Inhibition Kinetics and Emodin Cocrystal Structure of a Type II Polyketide Ketoreductase<sup>,</sup>. Biochemistry.

Chao Tu, Yu-Hong Tan, Gary Shaw, Zheng Zhou, Yawen Bai, Ray Luo, Xinhua Ji (2008). Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution. Acta Crystallographica Section D Biological Crystallography.

Ray Luo (2008). Hydrogen-Bonded Complexes in Chloroform: Affinity, Entropy, and Conformation. M S. Head, R Luo, J A. Given, M K. Gilson,.

Yu-Hong Tan, Chunhu Tan, Junmei Wang, Ray Luo (2008). Continuum Polarizable Force Field within the Poisson−Boltzmann Framework. The Journal of Physical Chemistry B.

Jun Wang, Chunhu Tan, Hai-Feng Chen, Ray Luo (2008). All-Atom Computer Simulations of Amyloid Fibrils Disaggregation. Biophysical Journal.

Qiang Lu, Yu-Hong Tan, Ray Luo (2007). Molecular Dynamics Simulations of p53 DNA-Binding Domain. The Journal of Physical Chemistry B.

Hai-Feng Chen, Ray Luo (2007). Binding Induced Folding in p53−MDM2 Complex. Journal of the American Chemical Society.

Chunhu Tan, Yu-Hong Tan, Ray Luo (2007). Implicit Nonpolar Solvent Models. The Journal of Physical Chemistry B.

Yu-Hong Tan, Ray Luo (2007). Continuum treatment of electronic polarization effect. The Journal of Chemical Physics.

Ray Luo (2007). AMBER5; University of California: San Francisco, CA. University of California: San Francisco, CA,.

Lijiang Yang, Chun-Hu Tan, Meng-Juei Hsieh, Junmei Wang, Yong Duan, Piotr Cieplak, James Caldwell, Peter A. Kollman, Ray Luo (2006). New-Generation Amber United-Atom Force Field. The Journal of Physical Chemistry B.

Thu Zar Lwin, Ruhong Zhou, Ray Luo (2006). Is Poisson-Boltzmann theory insufficient for protein folding simulations?. The Journal of Chemical Physics.

Chunhu Tan, Lijiang Yang, Ray Luo (2006). How Well Does Poisson−Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis. The Journal of Physical Chemistry B.

S. A. Danziger, S. J. Swamidass, Jue Zeng, L. R. Dearth, Qiang Lu, J. H. Chen, Jianlin Cheng, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, R. K. Brachmann, R. H. Lathrop (2006). Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Thu Zar Lwin, Ray Luo (2006). Force field influences in β‐hairpin folding simulations. Protein Science.

David A. Case, Thomas E. Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry.

Thur Zar Lwin, Ray Luo (2005). Overcoming entropic barrier with coupled sampling at dual resolutions. The Journal of Chemical Physics.

Ray Luo (2005). Nonpolar implicit solvent models. BIOPHYSICAL JOURNAL.

Ray Luo (2005). Computational prediction of p53 rescue; Effects of second-site rescue mutations on the stability of cancer mutants. BIOPHYSICAL JOURNAL.

Meng‐Juei Hsieh, Ray Luo (2004). Physical scoring function based on AMBER force field and Poisson–Boltzmann implicit solvent for protein structure prediction. Proteins: Structure, Function, and Bioinformatics.

Edward Z. Wen, Ray Luo (2004). Interplay of secondary structures and side-chain contacts in the denatured state of BBA1. The Journal of Chemical Physics.

Edward Z. Wen, Meng-Juei Hsieh, Peter A. Kollman, Ray Luo (2004). Enhanced ab initio protein folding simulations in Poisson–Boltzmann molecular dynamics with self-guiding forces. Journal of Molecular Graphics and Modelling.

Ray Luo (2003). From 1D to 3D: Cooperative Determination of a Protein’s Structure from its Sequence. University of California, Berkeley,.

Qiang Lu, Ray Luo (2003). A Poisson–Boltzmann dynamics method with nonperiodic boundary condition. The Journal of Chemical Physics.

Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James Caldwell, Junmei Wang, Peter Kollman (2003). A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations. Journal of Computational Chemistry.

Ray Luo, Laurent David, Michael K. Gilson (2002). Accelerated Poisson–Boltzmann calculations for static and dynamic systems. Journal of Computational Chemistry.

Ray Luo, Hillary S. R. Gilson, Michael J. Potter, Michael K. Gilson (2001). The Physical Basis of Nucleic Acid Base Stacking in Water. Biophysical Journal.

Laurent David, Ray Luo, Michael K. Gilson (2001). Ligand-receptor docking with the Mining Minima optimizer. Journal of Computer-Aided Molecular Design.

Kristy L. Mardis, Ray Luo, Michael K. Gilson (2001). Interpreting trends in the binding of cyclic ureas to HIV-1 protease. Journal of Molecular Biology.

Wei Wang, Wendell A. Lim, Araz Jakalian, Jian Wang, Junmei Wang, Ray Luo, Christopher I. Bayly, Peter A. Kollman (2001). An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis. Journal of the American Chemical Society.

Ray Luo, Michael K. Gilson (2000). Synthetic Adenine Receptors: Direct Calculation of Binding Affinity and Entropy. Journal of the American Chemical Society.

Kristy Mardis, Ray Luo, Laurent David, Michael Potter, Amy Glemza, Greg Payne, Michael K. Gilson (2000). Modeling Molecular Recognition: Theory and Application. Journal of Biomolecular Structure and Dynamics.

Laurent David, Ray Luo, Michael K. Gilson (2000). Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease. Journal of Computational Chemistry.

Ray Luo, Laurent David, Howard Hung, Judith Devaney, Michael K. Gilson (1999). Strength of Solvent-Exposed Salt-Bridges. The Journal of Physical Chemistry B.

Ray Luo, Martha S. Head, James A. Given, Michael K. Gilson (1999). Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation. Biophysical Chemistry.

Laurent David, Ray Luo, Martha S. Head, Michael K. Gilson (1999). Computational Study of KNI-272, a Potent Inhibitor of HIV-1 Protease: On the Mechanism of Preorganization. The Journal of Physical Chemistry B.

Ray Luo (1999). Calculation of the binding affinity of phenylalanine to beta-cyclodextrin. BIOPHYSICAL JOURNAL.

Rui Luo, Martha S. Head, John Moult, Michael K. Gilson (1998). p<i>K</i><sub>a</sub> Shifts in Small Molecules and HIV Protease: Electrostatics and Conformation. Journal of the American Chemical Society.

Ray Luo (1997). PROSTAR: The protein potential test site. Unpublished.

Rui Luo, John Moult, Michael K. Gilson (1997). Dielectric Screening Treatment of Electrostatic Solvation. The Journal of Physical Chemistry B.

Ram Samudrala, Jan T. Pedersen, Huai‐bei Zhou, Rui Luo, Krzysztof Fidelis, John Moult (1995). Confronting the problem of interconnected structural changes in the comparative modeling of proteins. Proteins: Structure, Function, and Bioinformatics.