Ray Luo

picture of Ray  Luo

Professor, Molecular Biology and Biochemistry
School of Biological Sciences

Professor, Biomedical Engineering
The Henry Samueli School of Engineering

Professor, Chemical Engineering & Materials Science
The Henry Samueli School of Engineering

B.S., Beijing University, 1990, Biophysics
Ph.D., University of Maryland at College Park, 1998, Chemistry

Phone: (949) 824-9528
Fax: (949) 824-8551
Email: ray.luo@uci.edu

University of California, Irvine
3206 Natural Sciences I
Mail Code: 3900
Irvine, CA 92697
Research Interests
Computational analysis of biomolecular sequence, structure, dynamics, and function.
Research Abstract
We use computational approaches to study biomolecular structures and functions. Our goal is to interpret the structural and functional information encoded in genomes and to understand life at the most fundamental level based on physical and chemical principles. Our current research effort focuses on developing reliable and efficient computational methods to study and predict structures, functions, and intermolecular interactions at atomic detail.
Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis, J Zhang, H Luo, H Liu, W Ye, R Luo, HF Chen, Scientific Reports, 6: 24587, 2016
D. R. Jackson, S. S. Tu, M. C. Nguyen, J. F. Barajas, A. J. Schaub, D. Krug, D. Pistorius, R. Luo, R. Mu¨ller, and S.-C. Tsai, Structural Insights Into Anthranilate Priming During Type II Polyketide Biosynthesis, ACS Chem. Biol., 11:95-103, 2015.
W. Ye, D. Ji, W. Wang, R. Luo, and H.-F. Chen, Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins, J. Chem. Inf. Model., 55:1021–1029, 2015.
Z. Li, L. Xiao, Q. Cai, H. Zhao, and R. Luo, A Semi-implicit Augmented IIM for Navier-Stokes Equations with Open, Traction, or Free Boundary Conditions, J. Comp. Phys., 297:182–193, 2015.
J. F. Barajas, R. M. Phelan, A. J. Schaub, J. T. Kliewer, P. J. Kelly, D. R. Jackson, R. Luo, J. D. Keasling, S.-C. Tsai, Comprehensive Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols, Chem. & Biol., 22:1018–1029, 2015.
W. M Botello-Smith and R. Luo, Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation, J. Chem. Inf. Model., 55:2187-2199, 2015.
W. Wang, W. Ye, C. Jiang, R. Luo, and H.F. Chen, New Force Field on Modeling Intrinsically Disordered Proteins, Chem. Biol. Drug Des., 84:253–269, 2014.
L. Xiao, Q. Cai, Z. Li, H. Zhao, and . Luo, A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation, Chem. Phys. Lett. 616-617:67–74, 2014.
L. Xiao, Q. Cai, X. Ye, J. Wang, and R. Luo, Electrostatics Forces in the Poisson-Boltzmann Systems, J. Chem. Phys., 139:094106, 2013.
J. Wang, Q. Cai, X. Ye, and R. Luo, Reducing Grid-Dependence in Finite-Difference Poisson-Boltzmann Calculations, J. Chem. Theo. Comp., 8:2741–2751, 2012.
J. Wang, P. Cieplak, Q. Cai, M. J. Hsieh, J. Wang, Y. Duan, R. Luo, Development of Polarizable Models for Molecular Mechanical Calculations III: Polarizable Water Models Conforming to Thole Polarization Screening Schemes, J. Phys. Chem., 116:7999–8008, 2012.
J. Wang, P. Cieplak, J. Li, Q. Cai, M. J. Hsieh, R. Luo, Y. Duan, Development of Polarizable Models for Molecular Mechanical Calculations IV: van der Waals parameterization, J. Phys. Chem., 116:7088–7101, 2012.
W. Ye, F. Qin, R. Luo, H. Chen, Atomistic Mechanism of microRNA Translation Upregulation via Molecular Dynamics Simulations, PLoS One, 7:43788, 2012.
Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies. Cai Q, Ye X, Wang J, Luo R. Chem Phys Lett. 2011 Oct;514(4-6):368-373.
Virtual screening using molecular simulations. Yang T, Wu JC, Yan C, Wang Y, Luo R, Gonzales MB, Dalby KN, Ren P. Proteins. 2011 Jun;79(6):1940-51. doi: 10.1002/prot.23018.
Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies, Wang J, Cieplak P, Li J, Wang J, Cai Q, Hsieh M, Lei H, Luo R, Duan Y, J Phys Chem B. 2011 Mar 31;115(12):3100-11.
Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability, Wang J, Cieplak P, Li J, Hou T, Luo R, Duan Y, J Phys Chem B. 2011 Mar 31;115(12):3091-9.
Balancing simulation accuracy and efficiency with the Amber united atom force field, Hsieh MJ, Luo R, J Phys Chem B. 2010 Mar 4;114(8):2886-93.
Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics, Wang J, Tan C, Chanco E, Luo R, Phys Chem Chem Phys. 2010 Feb 7;12(5):1194-202.
Assessment of linear finite-difference Poisson-Boltzmann solvers, Wang J, Luo R, J Comput Chem. 2010 Jun;31(8):1689-98
Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations, Tan YH, Chen YM, Ye X, Lu Q, Tretyachenko-Ladokhina V, Yang W, Senear DF, Luo R, Biophys Chem. 2009 Nov;145(1):37-44.
Structural and functional implications of p53 missense cancer mutations, Tan Y, Luo R, BMC Biophys. 2009 Jun 26;2(1):5
On removal of charge singularity in Poisson-Boltzmann equation, Cai Q, Wang J, Zhao HK, Luo R, J Chem Phys. 2009 Apr 14;130(14):145101.
All-atom computer simulations of amyloid fibrils disaggregation, Wang J, Tan C, Chen HF, Luo R, Biophys J. 2008 Dec;95(11):5037-47. Epub 2008 Aug 29.
Implicit nonpolar solvent models, Tan C, Tan YH, Luo R, J Phys Chem B. 2007 Oct 25;111(42):12263-74.
Continuum treatment of electronic polarization effect, Tan YH, Luo R, J Chem Phys. 2007 Mar 7;126(9):094103.
Binding Induced Folding in p53-MDM2 Complex, H. F. Chen and R. Luo, Journal of the Chemical Society, 129:2930-2937, 2007.
Professional Societies
Graduate Programs
Structural Biology and Molecular Biophysics

Biomedical Engineering

Medicinal Chemistry and Pharmacology

Mathematical and Computational Biology

Research Centers
Chemical and Structural Biology
Biomedical Engineering
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