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Luo, Ray

TitleProfessor
InstitutionUniversity of California, Irvine
DepartmentMolecular Biology & Biochem
Address3206 Natural Sciences I
Zot 3900
CA 92697
Phone(949) 824-9528, 9562
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    Collapse Research 
    Collapse Research Activities and Funding
    AMBER/PBSA: An Open-Source Computer Program for Accurate and Scalable Solvation Analysis of Biomolecules
    NIH/NIGMS R01GM093040May 1, 2010 - Jan 31, 2019
    Role: Principal Investigator
    AMBER force field consortium: a coherent biomolecular simulation platform
    NIH/NIGMS R01GM079383Sep 28, 2007 - Feb 28, 2018
    Role: Co-Principal Investigator
    Determinants of Folding Mechanism in Small Proteins
    NIH/NIGMS R01GM069620Aug 1, 2004 - Jul 31, 2010
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Liu H, Guo X, Han J, Luo R, Chen HF. Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB. J Chem Phys. 2018 Jun 14; 148(22):225101. PMID: 29907037.
      View in: PubMed
    2. Liu H, Song D, Lu H, Luo R, Chen HF. Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF. Chem Biol Drug Des. 2018 May 28. PMID: 29808548.
      View in: PubMed
    3. Greene D, Po T, Pan J, Tabibian T, Luo R. Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aß) Antibodies. J Phys Chem B. 2018 04 26; 122(16):4521-4536. PMID: 29617557.
      View in: PubMed
    4. Ellis BD, Milligan JC, White AR, Duong V, Altman PX, Mohammed LY, Crump MP, Crosby J, Luo R, Vanderwal CD, Tsai SC. An Oxetane-Based Polyketide Surrogate To Probe Substrate Binding in a Polyketide Synthase. J Am Chem Soc. 2018 Apr 18; 140(15):4961-4964. PMID: 29620883.
      View in: PubMed
    5. Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci. 2017; 4:87. PMID: 29367919.
      View in: PubMed
    6. Xiao L, Luo R. Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid. J Chem Phys. 2017 Dec 07; 147(21):214112. PMID: 29221408.
      View in: PubMed
    7. Wang C, Ren P, Luo R. Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling. J Phys Chem B. 2017 12 14; 121(49):11169-11179. PMID: 29164898.
      View in: PubMed
    8. Xiao L, Diao J, Greene D, Wang J, Luo R. A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins. J Chem Theory Comput. 2017 Jul 11; 13(7):3398-3412. PMID: 28564540.
      View in: PubMed
    9. Qi R, Botello-Smith WM, Luo R. Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units. J Chem Theory Comput. 2017 Jul 11; 13(7):3378-3387. PMID: 28553983.
      View in: PubMed
    10. Guo X, Han J, Luo R, Chen HF. Conformation Dynamics of the Intrinsically Disordered Protein c-Myb with the ff99IDPs Force Field. RSC Adv. 2017; 7(47):29713-29721. PMID: 29104751.
      View in: PubMed
    11. Song D, Luo R, Chen HF. The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. J Chem Inf Model. 2017 05 22; 57(5):1166-1178. PMID: 28448138.
      View in: PubMed
    12. Ye W, Qian T, Liu H, Luo R, Chen HF. Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. J Chem Inf Model. 2017 05 22; 57(5):1153-1165. PMID: 28425706.
      View in: PubMed
    13. Wang C, Xiao L, Luo R. Numerical interpretation of molecular surface field in dielectric modeling of solvation. J Comput Chem. 2017 May 30; 38(14):1057-1070. PMID: 28318096.
      View in: PubMed
    14. Qian T, Wo J, Zhang Y, Song Q, Feng G, Luo R, Lin S, Wu G, Chen HF. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode. Sci Rep. 2017 Jan 11; 7:40254. PMID: 28074848.
      View in: PubMed
    15. Zhang JM, Jiang C, Ye W, Luo R, Chen HF. Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network. Mol Biosyst. 2016 Dec 20; 13(1):156-164. PMID: 27841427.
      View in: PubMed
    16. Greene D, Botello-Smith WM, Follmer A, Xiao L, Lambros E, Luo R. Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor. J Phys Chem B. 2016 12 08; 120(48):12293-12304. PMID: 27934233.
      View in: PubMed
    17. Song D, Wang W, Ye W, Ji D, Luo R, Chen HF. ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins. Chem Biol Drug Des. 2017 Jan; 89(1):5-15. PMID: 27484738.
      View in: PubMed
    18. Wang C, Nguyen PH, Pham K, Huynh D, Le TB, Wang H, Ren P, Luo R. Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. J Comput Chem. 2016 Oct 15; 37(27):2436-46. PMID: 27510546; PMCID: PMC5018451 [Available on 10/15/17].
    19. Wang W, Jiang C, Zhang J, Ye W, Luo R, Chen HF. Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Sci Rep. 2016 08 03; 6:31005. PMID: 27484311.
      View in: PubMed
    20. Yang J, Liu H, Liu X, Gu C, Luo R, Chen HF. Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. J Chem Inf Model. 2016 06 27; 56(6):1184-1192. PMID: 27227511.
      View in: PubMed
    21. Xiao L, Wang C, Ye X, Luo R. Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions. J Phys Chem B. 2016 08 25; 120(33):8707-21. PMID: 27146097.
      View in: PubMed
    22. Zhang J, Luo H, Liu H, Ye W, Luo R, Chen HF. Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Sci Rep. 2016 Apr 15; 6:24587. PMID: 27079666; PMCID: PMC4832343.
    23. Jackson DR, Tu SS, Nguyen M, Barajas JF, Schaub AJ, Krug D, Pistorius D, Luo R, Müller R, Tsai SC. Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis. ACS Chem Biol. 2016 Jan 15; 11(1):95-103. PMID: 26473393.
      View in: PubMed
    24. Botello-Smith WM, Luo R. Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation. J Chem Inf Model. 2015 Oct 26; 55(10):2187-99. PMID: 26389966; PMCID: PMC4720152.
    25. Barajas JF, Phelan RM, Schaub AJ, Kliewer JT, Kelly PJ, Jackson DR, Luo R, Keasling JD, Tsai SC. Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols. Chem Biol. 2015 Aug 20; 22(8):1018-29. PMID: 26235055.
      View in: PubMed
    26. Li Z, Xiao L, Cai Q, Zhao H, Luo R. A semi-implicit augmented IIM for Navier-Stokes equations with open, traction, or free boundary conditions. J Comput Phys. 2015 Aug 15; 297:182-193. PMID: 27087702.
      View in: PubMed
    27. Ye W, Ji D, Wang W, Luo R, Chen HF. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. J Chem Inf Model. 2015 May 26; 55(5):1021-9. PMID: 25919886.
      View in: PubMed
    28. Xu L, Ye W, Jiang C, Yang J, Zhang J, Feng Y, Luo R, Chen HF. Recognition mechanism between Lac repressor and DNA with correlation network analysis. J Phys Chem B. 2015 Feb 19; 119(7):2844-56. PMID: 25633018.
      View in: PubMed
    29. Xiao L, Cai Q, Li Z, Zhao H, Luo R. A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation. Chem Phys Lett. 2014 Nov 25; 616-617:67-74. PMID: 25404761.
      View in: PubMed
    30. Yu Q, Ye W, Jiang C, Luo R, Chen HF. Specific recognition mechanism between RNA and the KH3 domain of Nova-2 protein. J Phys Chem B. 2014 Oct 30; 118(43):12426-34. PMID: 25300025.
      View in: PubMed
    31. Wang W, Ye W, Jiang C, Luo R, Chen HF. New force field on modeling intrinsically disordered proteins. Chem Biol Drug Des. 2014 Sep; 84(3):253-69. PMID: 24589355.
      View in: PubMed
    32. Wang C, Wang J, Cai Q, Li Z, Zhao HK, Luo R. Exploring accurate Poisson-Boltzmann methods for biomolecular simulations. Comput Theor Chem. 2013 Nov 15; 1024:34-44. PMID: 24443709.
      View in: PubMed
    33. Ye W, Yang J, Yu Q, Wang W, Hancy J, Luo R, Chen HF. Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations. Phys Chem Chem Phys. 2013 Nov 14; 15(42):18510-22. PMID: 24072031.
      View in: PubMed
    34. Xiao L, Cai Q, Ye X, Wang J, Luo R. Electrostatic forces in the Poisson-Boltzmann systems. J Chem Phys. 2013 Sep 07; 139(9):094106. PMID: 24028101; PMCID: PMC3779268.
    35. Wang W, Ye W, Yu Q, Jiang C, Zhang J, Luo R, Chen HF. Conformational selection and induced fit in specific antibody and antigen recognition: SPE7 as a case study. J Phys Chem B. 2013 May 02; 117(17):4912-23. PMID: 23548180.
      View in: PubMed
    36. Liu X, Wang C, Wang J, Li Z, Zhao H, Luo R. Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications. Phys Chem Chem Phys. 2013 Jan 07; 15(1):129-41. PMID: 23147243; PMCID: PMC3518737.
    37. Botello-Smith WM, Liu X, Cai Q, Li Z, Zhao H, Luo R. Numerical Poisson-Boltzmann Model for Continuum Membrane Systems. Chem Phys Lett. 2013 Jan 03; 555:274-281. PMID: 23439886.
      View in: PubMed
    38. Cai Q, Ye X, Luo R. Dielectric pressure in continuum electrostatic solvation of biomolecules. Phys Chem Chem Phys. 2012 Dec 05; 14(45):15917-25. PMID: 23093365.
      View in: PubMed
    39. Ye W, Qin F, Zhang J, Luo R, Chen HF. Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations. PLoS One. 2012; 7(8):e43788. PMID: 22952765; PMCID: PMC3428290.
    40. Wang J, Cieplak P, Cai Q, Hsieh MJ, Wang J, Duan Y, Luo R. Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes. J Phys Chem B. 2012 Jul 19; 116(28):7999-8008. PMID: 22712654; PMCID: PMC3493849.
    41. Wang J, Cai Q, Xiang Y, Luo R. Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations. J Chem Theory Comput. 2012 Aug 14; 8(8):2741-2751. PMID: 23185142.
      View in: PubMed
    42. Wang J, Cieplak P, Li J, Cai Q, Hsieh MJ, Luo R, Duan Y. Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization. J Phys Chem B. 2012 Jun 21; 116(24):7088-101. PMID: 22612331; PMCID: PMC3391542.
    43. Cai Q, Ye X, Wang J, Luo R. On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods. J Chem Theory Comput. 2011 Nov 01; 7(11):3608-3619. PMID: 24772042.
      View in: PubMed
    44. Cai Q, Ye X, Wang J, Luo R. Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies. Chem Phys Lett. 2011 Oct; 514(4-6):368-373. PMID: 22125339.
      View in: PubMed
    45. Yang T, Wu JC, Yan C, Wang Y, Luo R, Gonzales MB, Dalby KN, Ren P. Virtual screening using molecular simulations. Proteins. 2011 Jun; 79(6):1940-51. PMID: 21491494; PMCID: PMC3092865.
    46. Wang J, Cieplak P, Li J, Wang J, Cai Q, Hsieh M, Lei H, Luo R, Duan Y. Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies. J Phys Chem B. 2011 Mar 31; 115(12):3100-11. PMID: 21391583; PMCID: PMC3082585.
    47. Wang J, Cieplak P, Li J, Hou T, Luo R, Duan Y. Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability. J Phys Chem B. 2011 Mar 31; 115(12):3091-9. PMID: 21391553; PMCID: PMC3082581.
    48. Hsieh MJ, Luo R. Exploring a coarse-grained distributive strategy for finite-difference Poisson-Boltzmann calculations. J Mol Model. 2011 Aug; 17(8):1985-96. PMID: 21127924; PMCID: PMC3143316.
    49. Wang J, Luo R. Assessment of linear finite-difference Poisson-Boltzmann solvers. J Comput Chem. 2010 Jun; 31(8):1689-98. PMID: 20063271; PMCID: PMC2854862.
    50. Ye X, Wang J, Luo R. A revised density function for molecular surface definition in continuum solvent models. J Chem Theory Comput. 2010 Apr 13; 6(4):1157-1169. PMID: 24723844.
      View in: PubMed
    51. Hsieh MJ, Luo R. Balancing simulation accuracy and efficiency with the Amber united atom force field. J Phys Chem B. 2010 Mar 04; 114(8):2886-93. PMID: 20131885.
      View in: PubMed
    52. Cai Q, Hsieh MJ, Wang J, Luo R. Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers. J Chem Theory Comput. 2010 Jan 12; 6(1):203-211. PMID: 24723843.
      View in: PubMed
    53. Wang J, Tan C, Chanco E, Luo R. Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics. Phys Chem Chem Phys. 2010 Feb 07; 12(5):1194-202. PMID: 20094685.
      View in: PubMed
    54. Tan YH, Chen YM, Ye X, Lu Q, Tretyachenko-Ladokhina V, Yang W, Senear DF, Luo R. Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations. Biophys Chem. 2009 Nov; 145(1):37-44. PMID: 19748724; PMCID: PMC2794655.
    55. Ye X, Cai Q, Yang W, Luo R. Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method. Biophys J. 2009 Jul 22; 97(2):554-62. PMID: 19619470; PMCID: PMC2711334.
    56. Tan Y, Luo R. Structural and functional implications of p53 missense cancer mutations. PMC Biophys. 2009 Jun 26; 2(1):5. PMID: 19558684; PMCID: PMC2709103.
    57. Cai Q, Wang J, Zhao HK, Luo R. On removal of charge singularity in Poisson-Boltzmann equation. J Chem Phys. 2009 Apr 14; 130(14):145101. PMID: 19368474.
      View in: PubMed
    58. Wang J, Cai Q, Li ZL, Zhao HK, Luo R. Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision with Finite-Difference Algorithms. Chem Phys Lett. 2009 Jan 22; 468(4-6):112-118. PMID: 20098487.
      View in: PubMed
    59. Wang J, Tan C, Chen HF, Luo R. All-atom computer simulations of amyloid fibrils disaggregation. Biophys J. 2008 Dec; 95(11):5037-47. PMID: 18757563; PMCID: PMC2586582.
    60. Tan YH, Tan C, Wang J, Luo R. Continuum polarizable force field within the Poisson-Boltzmann framework. J Phys Chem B. 2008 Jun 26; 112(25):7675-88. PMID: 18507452; PMCID: PMC2495006.
    61. Tu C, Tan YH, Shaw G, Zhou Z, Bai Y, Luo R, Ji X. Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 angstroms resolution. Acta Crystallogr D Biol Crystallogr. 2008 May; 64(Pt 5):471-7. PMID: 18453682; PMCID: PMC2631104.
    62. Tan YH, Luo R. Protein stability prediction: a Poisson-Boltzmann approach. J Phys Chem B. 2008 Feb 14; 112(6):1875-83. PMID: 18211063.
      View in: PubMed
    63. Korman TP, Tan YH, Wong J, Luo R, Tsai SC. Inhibition kinetics and emodin cocrystal structure of a type II polyketide ketoreductase. Biochemistry. 2008 Feb 19; 47(7):1837-47. PMID: 18205400; PMCID: PMC2263082.
    64. Tan C, Tan YH, Luo R. Implicit nonpolar solvent models. J Phys Chem B. 2007 Oct 25; 111(42):12263-74. PMID: 17918880.
      View in: PubMed
    65. Lu Q, Tan YH, Luo R. Molecular dynamics simulations of p53 DNA-binding domain. J Phys Chem B. 2007 Oct 04; 111(39):11538-45. PMID: 17824689; PMCID: PMC2522240.
    66. Tan YH, Luo R. Continuum treatment of electronic polarization effect. J Chem Phys. 2007 Mar 07; 126(9):094103. PMID: 17362100.
      View in: PubMed
    67. Chen HF, Luo R. Binding induced folding in p53-MDM2 complex. J Am Chem Soc. 2007 Mar 14; 129(10):2930-7. PMID: 17302414; PMCID: PMC2528056.
    68. Lwin TZ, Luo R. Force field influences in beta-hairpin folding simulations. Protein Sci. 2006 Nov; 15(11):2642-55. PMID: 17075138; PMCID: PMC2242415.
    69. Tan C, Yang L, Luo R. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis. J Phys Chem B. 2006 Sep 21; 110(37):18680-7. PMID: 16970499.
      View in: PubMed
    70. Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R. New-generation amber united-atom force field. J Phys Chem B. 2006 Jul 06; 110(26):13166-76. PMID: 16805629.
      View in: PubMed
    71. Danziger SA, Swamidass SJ, Zeng J, Dearth LR, Lu Q, Chen JH, Cheng J, Hoang VP, Saigo H, Luo R, Baldi P, Brachmann RK, Lathrop RH. Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants. IEEE/ACM Trans Comput Biol Bioinform. 2006 Apr-Jun; 3(2):114-25. PMID: 17048398; PMCID: PMC2748235.
    72. Lwin TZ, Zhou R, Luo R. Is Poisson-Boltzmann theory insufficient for protein folding simulations? J Chem Phys. 2006 Jan 21; 124(3):034902. PMID: 16438609.
      View in: PubMed
    73. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem. 2005 Dec; 26(16):1668-88. PMID: 16200636; PMCID: PMC1989667.
    74. Lwin TZ, Luo R. Overcoming entropic barrier with coupled sampling at dual resolutions. J Chem Phys. 2005 Nov 15; 123(19):194904. PMID: 16321110.
      View in: PubMed
    75. Hsieh MJ, Luo R. Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction. Proteins. 2004 Aug 15; 56(3):475-86. PMID: 15229881.
      View in: PubMed
    76. Wen EZ, Luo R. Interplay of secondary structures and side-chain contacts in the denatured state of BBA1. J Chem Phys. 2004 Aug 01; 121(5):2412-21. PMID: 15260796.
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    77. Wen EZ, Hsieh MJ, Kollman PA, Luo R. Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces. J Mol Graph Model. 2004 May; 22(5):415-24. PMID: 15099837.
      View in: PubMed
    78. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem. 2003 Dec; 24(16):1999-2012. PMID: 14531054.
      View in: PubMed
    79. Luo R, David L, Gilson MK. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem. 2002 Oct; 23(13):1244-53. PMID: 12210150.
      View in: PubMed
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