Ray Luo

Title(s)Professor, Molecular Biology & Biochemistry
SchoolSchool of Biological Sciences
Address3206 Natural Sciences I
Zot 3900
Irvine CA 92697
Phone(949) 824-9528, 9562
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    Collapse Research 
    Collapse Research Activities and Funding
    Multi-scaled Modeling of Electrostatic and Polarization Effects in Biomolecules
    NIH R35GM130367Sep 1, 2019 - Aug 31, 2024
    Role: Principal Investigator
    AMBER/PBSA: An Open-Source Computer Program for Accurate and Scalable Solvation Analysis of Biomolecules
    NIH R01GM093040May 1, 2010 - Jan 31, 2020
    Role: Principal Investigator
    AMBER force field consortium: a coherent biomolecular simulation platform
    NIH R01GM079383Sep 28, 2007 - Feb 29, 2020
    Role: Co-Principal Investigator
    Determinants of Folding Mechanism in Small Proteins
    NIH 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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Understanding and fine tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine. Phys Chem Chem Phys. 2024 Apr 03; 26(14):10568-10578. Zhu Q, Wu Y, Luo R. PMID: 38512104.
      View in: PubMed   Mentions:    Fields:    
    2. PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents. J Chem Theory Comput. 2024 Apr 09; 20(7):2820-2829. Duan Y, Niu T, Wang J, Cieplak P, Luo R. PMID: 38502776; PMCID: PMC11008095.
      View in: PubMed   Mentions:    Fields:    
    3. Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model. J Chem Theory Comput. 2024 Mar 12; 20(5):2098-2110. Zhao S, Cieplak P, Duan Y, Luo R. PMID: 38394331.
      View in: PubMed   Mentions:    Fields:    
    4. AmberTools. J Chem Inf Model. 2023 Oct 23; 63(20):6183-6191. Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O'Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM. PMID: 37805934; PMCID: PMC10598796.
      View in: PubMed   Mentions: 12     Fields:    
    5. Grid-Robust Efficient Neural Interface Model for Universal Molecule Surface Construction from Point Clouds. J Phys Chem Lett. 2023 Oct 12; 14(40):9034-9041. Wu Y, Wei H, Zhu Q, Luo R. PMID: 37782231; PMCID: PMC10577766.
      View in: PubMed   Mentions:    Fields:    
    6. Streamlining and Optimizing Strategies of Electrostatic Parameterization. J Chem Theory Comput. 2023 Sep 26; 19(18):6353-6365. Zhu Q, Wu Y, Zhao S, Cieplak P, Duan Y, Luo R. PMID: 37676646; PMCID: PMC10530599.
      View in: PubMed   Mentions: 1     Fields:    
    7. Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions. Cell Chem Biol. 2023 11 16; 30(11):1478-1487.e7. Ji H, Lu X, Zhao S, Wang Q, Liao B, Bauer LG, Huber KVM, Luo R, Tian R, Tan CSH. PMID: 37652024; PMCID: PMC10840709.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    8. Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models. J Chem Theory Comput. 2023 Aug 08; 19(15):5047-5057. Huang Z, Zhao S, Cieplak P, Duan Y, Luo R, Wei H. PMID: 37441805; PMCID: PMC10434752.
      View in: PubMed   Mentions: 1     Fields:    
    9. Recent Advances in Biomolecular Recognition. Int J Mol Sci. 2023 May 05; 24(9). Zhu Q, Luo R. PMID: 37176015; PMCID: PMC10179535.
      View in: PubMed   Mentions:    Fields:    
    10. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov. 2023 03; 18(3):315-333. Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. PMID: 36715303; PMCID: PMC10149343.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    11. Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model. J Chem Theory Comput. 2023 Feb 14; 19(3):924-941. Zhao S, Cieplak P, Duan Y, Luo R. PMID: 36696564; PMCID: PMC10152989.
      View in: PubMed   Mentions: 2     Fields:    
    12. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nat Commun. 2022 11 26; 13(1):7282. King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. PMID: 36435948; PMCID: PMC9701214.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    13. Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model. J Chem Theory Comput. 2022 Oct 11; 18(10):6172-6188. Zhao S, Wei H, Cieplak P, Duan Y, Luo R. PMID: 36094401; PMCID: PMC10152986.
      View in: PubMed   Mentions: 3     Fields:    
    14. Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nat Commun. 2022 08 26; 13(1):5021. Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H. PMID: 36028482; PMCID: PMC9418148.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    15. Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power. ACS Catal. 2022 Jul 15; 12(14):8582-8592. King E, Cui Y, Aspacio D, Nicklen F, Zhang L, Maxel S, Luo R, Siegel JB, Aitchison E, Li H. PMID: 37622090; PMCID: PMC10449333.
      View in: PubMed   Mentions:
    16. PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields. J Chem Theory Comput. 2022 Jun 14; 18(6):3654-3670. Zhao S, Wei H, Cieplak P, Duan Y, Luo R. PMID: 35537209; PMCID: PMC9198001.
      View in: PubMed   Mentions: 5     Fields:    
    17. Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations. ACS Omega. 2022 May 03; 7(17):15132-15144. Khurshid B, Rehman AU, Luo R, Khan A, Wadood A, Anwar J. PMID: 35572757; PMCID: PMC9089684.
      View in: PubMed   Mentions: 3  
    18. Stress tensor and constant pressure simulation for polarizable Gaussian multipole model. J Chem Phys. 2022 Mar 21; 156(11):114114. Wei H, Cieplak P, Duan Y, Luo R. PMID: 35317572; PMCID: PMC9088672.
      View in: PubMed   Mentions: 6     Fields:    
    19. Motif-dependent immune co-receptor interactome profiling by photoaffinity chemical proteomics. Cell Chem Biol. 2022 06 16; 29(6):1024-1036.e5. Chen X, Ji S, Liu Z, Yuan X, Xu C, Qi R, He A, Zhao H, Song H, Xiao C, Gao W, Chen PR, Luo R, Li P, Wang F, Yang X, Tian R. PMID: 35093210.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    20. The Hippo pathway kinases LATS1 and LATS2 attenuate cellular responses to heavy metals through phosphorylating MTF1. Nat Cell Biol. 2022 01; 24(1):74-87. Han H, Nakaoka HJ, Hofmann L, Zhou JJ, Yu C, Zeng L, Nan J, Seo G, Vargas RE, Yang B, Qi R, Bardwell L, Fishman DA, Cho KWY, Huang L, Luo R, Warrior R, Wang W. PMID: 35027733; PMCID: PMC9022944.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    21. Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations. J Chem Theory Comput. 2021 Oct 12; 17(10):6214-6224. Wei H, Zhao Z, Luo R. PMID: 34516109; PMCID: PMC9132718.
      View in: PubMed   Mentions: 4     Fields:    
    22. Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst. ACS Synth Biol. 2021 09 17; 10(9):2359-2370. Maxel S, Saleh S, King E, Aspacio D, Zhang L, Luo R, Li H. PMID: 34469126; PMCID: PMC10362907.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    23. Recent Developments in Free Energy Calculations for Drug Discovery. Front Mol Biosci. 2021; 8:712085. King E, Aitchison E, Li H, Luo R. PMID: 34458321; PMCID: PMC8387144.
      View in: PubMed   Mentions: 25  
    24. Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. J Chem Theory Comput. 2021 Apr 13; 17(4):2541-2555. King E, Qi R, Li H, Luo R, Aitchison E. PMID: 33764050; PMCID: PMC8254375.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    25. Recent Force Field Strategies for Intrinsically Disordered Proteins. J Chem Inf Model. 2021 03 22; 61(3):1037-1047. Mu J, Liu H, Zhang J, Luo R, Chen HF. PMID: 33591749; PMCID: PMC8256680.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    26. Development of a Pantetheine Force Field Library for Molecular Modeling. J Chem Inf Model. 2021 02 22; 61(2):856-868. Zhao S, Schaub AJ, Tsai SC, Luo R. PMID: 33534558; PMCID: PMC8266206.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    27. Molecular Basis for Polyketide Ketoreductase-Substrate Interactions. Int J Mol Sci. 2020 Oct 13; 21(20). Zhao S, Ni F, Qiu T, Wolff JT, Tsai SC, Luo R. PMID: 33066287; PMCID: PMC7588967.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    28. Leveraging Oxidative Stress to Regulate Redox Balance-Based, In Vivo Growth Selections for Oxygenase Engineering. ACS Synth Biol. 2020 11 20; 9(11):3124-3133. Maxel S, King E, Zhang Y, Luo R, Li H. PMID: 32966747; PMCID: PMC10441625.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    29. Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations. J Chem Phys. 2020 Sep 21; 153(11):114116. Wei H, Qi R, Wang J, Cieplak P, Duan Y, Luo R. PMID: 32962395; PMCID: PMC7502018.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    30. In Vivo, High-Throughput Selection of Thermostable Cyclohexanone Monooxygenase (CHMO). Catalysts. 2020 Aug; 10(8). Maxel S, Zhang L, King E, Acosta AP, Luo R, Li H. PMID: 37637965; PMCID: PMC10453637.
      View in: PubMed   Mentions:
    31. Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. J Chem Inf Model. 2020 04 27; 60(4):2257-2267. Song D, Liu H, Luo R, Chen HF. PMID: 32227937; PMCID: PMC10449432.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    32. Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor. EMBO J. 2020 01 02; 39(1):e102406. Vargas RE, Duong VT, Han H, Ta AP, Chen Y, Zhao S, Yang B, Seo G, Chuc K, Oh S, El Ali A, Razorenova OV, Chen J, Luo R, Li X, Wang W. PMID: 31782549; PMCID: PMC6939200.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    33. Well-Balanced Force Field ff03CMAP for Folded and Disordered Proteins. J Chem Theory Comput. 2019 Dec 10; 15(12):6769-6780. Zhang Y, Liu H, Yang S, Luo R, Chen HF. PMID: 31657215; PMCID: PMC7196277.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    34. Dynamical important residue network (DIRN): network inference via conformational change. Bioinformatics. 2019 11 01; 35(22):4664-4670. Li Q, Luo R, Chen HF. PMID: 31038692; PMCID: PMC6853687.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    35. Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins. Phys Chem Chem Phys. 2019 Oct 09; 21(39):21918-21931. Liu H, Song D, Zhang Y, Yang S, Luo R, Chen HF. PMID: 31552948; PMCID: PMC7198049.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    36. Improved Poisson-Boltzmann Methods for High-Performance Computing. J Chem Theory Comput. 2019 Nov 12; 15(11):6190-6202. Wei H, Luo A, Qiu T, Luo R, Qi R. PMID: 31525962; PMCID: PMC7194241.
      View in: PubMed   Mentions: 6     Fields:    
    37. Molecular basis for interactions between an acyl carrier protein and a ketosynthase. Nat Chem Biol. 2019 07; 15(7):669-671. Milligan JC, Lee DJ, Jackson DR, Schaub AJ, Beld J, Barajas JF, Hale JJ, Luo R, Burkart MD, Tsai SC. PMID: 31209348; PMCID: PMC7323458.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    38. Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. J Chem Inf Model. 2019 06 24; 59(6):3041-3056. Greene D, Qi R, Nguyen R, Qiu T, Luo R. PMID: 31145610; PMCID: PMC7197397.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    39. Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases. Methods Enzymol. 2019; 622:375-409. Schaub AJ, Moreno GO, Zhao S, Truong HV, Luo R, Tsai SC. PMID: 31155062; PMCID: PMC7197764.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    40. An efficient second-order poisson-boltzmann method. J Comput Chem. 2019 05 05; 40(12):1257-1269. Wei H, Luo R, Qi R. PMID: 30776135; PMCID: PMC6422926.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    41. Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy. J Chem Theory Comput. 2019 Feb 12; 15(2):1146-1158. Wang J, Cieplak P, Luo R, Duan Y. PMID: 30645118; PMCID: PMC7197406.
      View in: PubMed   Mentions: 15     Fields:    
    42. Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units. J Chem Inf Model. 2019 01 28; 59(1):409-420. Qi R, Luo R. PMID: 30550277; PMCID: PMC6430105.
      View in: PubMed   Mentions: 6     Fields:    
    43. Engineering a Coenzyme A Detour To Expand the Product Scope and Enhance the Selectivity of the Ehrlich Pathway. ACS Synth Biol. 2018 12 21; 7(12):2758-2764. Black WB, King E, Wang Y, Jenic A, Rowley AT, Seki K, Luo R, Li H. PMID: 30433765; PMCID: PMC7195871.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    44. Computational Studies of Intrinsically Disordered Proteins. J Phys Chem B. 2018 11 21; 122(46):10455-10469. Duong VT, Chen Z, Thapa MT, Luo R. PMID: 30372613; PMCID: PMC6249069.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    45. Regulation of the Hippo Pathway by Phosphatidic Acid-Mediated Lipid-Protein Interaction. Mol Cell. 2018 10 18; 72(2):328-340.e8. Han H, Qi R, Zhou JJ, Ta AP, Yang B, Nakaoka HJ, Seo G, Guan KL, Luo R, Wang W. PMID: 30293781; PMCID: PMC6195446.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    46. Intrinsically disordered protein-specific force field CHARMM36IDPSFF. Chem Biol Drug Des. 2018 10; 92(4):1722-1735. Liu H, Song D, Lu H, Luo R, Chen HF. PMID: 29808548.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    47. Development of a High-Throughput, In Vivo Selection Platform for NADPH-Dependent Reactions Based on Redox Balance Principles. ACS Synth Biol. 2018 07 20; 7(7):1715-1721. Zhang L, King E, Luo R, Li H. PMID: 29939709; PMCID: PMC7195872.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    48. Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB. J Chem Phys. 2018 Jun 14; 148(22):225101. Liu H, Guo X, Han J, Luo R, Chen HF. PMID: 29907037; PMCID: PMC7156114.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    49. Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies. J Phys Chem B. 2018 04 26; 122(16):4521-4536. Greene D, Po T, Pan J, Tabibian T, Luo R. PMID: 29617557; PMCID: PMC5927393.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    50. An Oxetane-Based Polyketide Surrogate To Probe Substrate Binding in a Polyketide Synthase. J Am Chem Soc. 2018 04 18; 140(15):4961-4964. Ellis BD, Milligan JC, White AR, Duong V, Altman PX, Mohammed LY, Crump MP, Crosby J, Luo R, Vanderwal CD, Tsai SC. PMID: 29620883; PMCID: PMC6625825.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    51. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci. 2017; 4:87. Wang C, Greene D, Xiao L, Qi R, Luo R. PMID: 29367919; PMCID: PMC5768160.
      View in: PubMed   Mentions: 135  
    52. 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. Xiao L, Luo R. PMID: 29221408; PMCID: PMC5720894.
      View in: PubMed   Mentions: 2     Fields:    
    53. Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling. J Phys Chem B. 2017 12 14; 121(49):11169-11179. Wang C, Ren P, Luo R. PMID: 29164898; PMCID: PMC5730473.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    54. A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins. J Chem Theory Comput. 2017 Jul 11; 13(7):3398-3412. Xiao L, Diao J, Greene D, Wang J, Luo R. PMID: 28564540; PMCID: PMC5728381.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    55. Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units. J Chem Theory Comput. 2017 Jul 11; 13(7):3378-3387. Qi R, Botello-Smith WM, Luo R. PMID: 28553983; PMCID: PMC5728380.
      View in: PubMed   Mentions: 9     Fields:    
    56. Conformation Dynamics of the Intrinsically Disordered Protein c-Myb with the ff99IDPs Force Field. RSC Adv. 2017; 7(47):29713-29721. Guo X, Han J, Luo R, Chen HF. PMID: 29104751; PMCID: PMC5665395.
      View in: PubMed   Mentions: 8  
    57. 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. Song D, Luo R, Chen HF. PMID: 28448138; PMCID: PMC5731455.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
    58. Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. J Chem Inf Model. 2017 05 22; 57(5):1153-1165. Ye W, Qian T, Liu H, Luo R, Chen HF. PMID: 28425706; PMCID: PMC5730271.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    59. Numerical interpretation of molecular surface field in dielectric modeling of solvation. J Comput Chem. 2017 05 30; 38(14):1057-1070. Wang C, Xiao L, Luo R. PMID: 28318096; PMCID: PMC5464005.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    60. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode. Sci Rep. 2017 01 11; 7:40254. Qian T, Wo J, Zhang Y, Song Q, Feng G, Luo R, Lin S, Wu G, Chen HF. PMID: 28074848; PMCID: PMC5225493.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    61. Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network. Mol Biosyst. 2016 Dec 20; 13(1):156-164. Zhang JM, Jiang C, Ye W, Luo R, Chen HF. PMID: 27841427; PMCID: PMC5173395.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    62. Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor. J Phys Chem B. 2016 12 08; 120(48):12293-12304. Greene D, Botello-Smith WM, Follmer A, Xiao L, Lambros E, Luo R. PMID: 27934233; PMCID: PMC5460638.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    63. ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins. Chem Biol Drug Des. 2017 Jan; 89(1):5-15. Song D, Wang W, Ye W, Ji D, Luo R, Chen HF. PMID: 27484738; PMCID: PMC5480619.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    64. Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. J Comput Chem. 2016 10 15; 37(27):2436-46. Wang C, Nguyen PH, Pham K, Huynh D, Le TB, Wang H, Ren P, Luo R. PMID: 27510546; PMCID: PMC5018451.
      View in: PubMed   Mentions: 66     Fields:    Translation:Cells
    65. Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Sci Rep. 2016 08 03; 6:31005. Wang W, Jiang C, Zhang J, Ye W, Luo R, Chen HF. PMID: 27484311; PMCID: PMC4971525.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    66. 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. Yang J, Liu H, Liu X, Gu C, Luo R, Chen HF. PMID: 27227511; PMCID: PMC5115163.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    67. 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. Xiao L, Wang C, Ye X, Luo R. PMID: 27146097; PMCID: PMC5115882.
      View in: PubMed   Mentions: 5     Fields:    
    68. Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Sci Rep. 2016 Apr 15; 6:24587. Zhang J, Luo H, Liu H, Ye W, Luo R, Chen HF. PMID: 27079666; PMCID: PMC4832343.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    69. Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis. ACS Chem Biol. 2016 Jan 15; 11(1):95-103. Jackson DR, Tu SS, Nguyen M, Barajas JF, Schaub AJ, Krug D, Pistorius D, Luo R, Müller R, Tsai SC. PMID: 26473393; PMCID: PMC7886370.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    70. 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. Botello-Smith WM, Luo R. PMID: 26389966; PMCID: PMC4720152.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    71. 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. Barajas JF, Phelan RM, Schaub AJ, Kliewer JT, Kelly PJ, Jackson DR, Luo R, Keasling JD, Tsai SC. PMID: 26235055.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    72. 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. Li Z, Xiao L, Cai Q, Zhao H, Luo R. PMID: 27087702; PMCID: PMC4830499.
      View in: PubMed   Mentions: 5  
    73. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. J Chem Inf Model. 2015 May 26; 55(5):1021-9. Ye W, Ji D, Wang W, Luo R, Chen HF. PMID: 25919886; PMCID: PMC5490450.
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    74. Recognition mechanism between Lac repressor and DNA with correlation network analysis. J Phys Chem B. 2015 Feb 19; 119(7):2844-56. Xu L, Ye W, Jiang C, Yang J, Zhang J, Feng Y, Luo R, Chen HF. PMID: 25633018.
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    75. 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. Xiao L, Cai Q, Li Z, Zhao H, Luo R. PMID: 25404761; PMCID: PMC4231827.
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    76. Specific recognition mechanism between RNA and the KH3 domain of Nova-2 protein. J Phys Chem B. 2014 Oct 30; 118(43):12426-34. Yu Q, Ye W, Jiang C, Luo R, Chen HF. PMID: 25300025.
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    77. New force field on modeling intrinsically disordered proteins. Chem Biol Drug Des. 2014 Sep; 84(3):253-69. Wang W, Ye W, Jiang C, Luo R, Chen HF. PMID: 24589355.
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    78. Exploring accurate Poisson-Boltzmann methods for biomolecular simulations. Comput Theor Chem. 2013 Nov 15; 1024:34-44. Wang C, Wang J, Cai Q, Li Z, Zhao HK, Luo R. PMID: 24443709; PMCID: PMC3891588.
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    79. Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations. Phys Chem Chem Phys. 2013 Nov 14; 15(42):18510-22. Ye W, Yang J, Yu Q, Wang W, Hancy J, Luo R, Chen HF. PMID: 24072031.
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    80. Electrostatic forces in the Poisson-Boltzmann systems. J Chem Phys. 2013 Sep 07; 139(9):094106. Xiao L, Cai Q, Ye X, Wang J, Luo R. PMID: 24028101; PMCID: PMC3779268.
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    81. 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. Wang W, Ye W, Yu Q, Jiang C, Zhang J, Luo R, Chen HF. PMID: 23548180.
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    82. 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. Liu X, Wang C, Wang J, Li Z, Zhao H, Luo R. PMID: 23147243; PMCID: PMC3518737.
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    83. Numerical Poisson-Boltzmann Model for Continuum Membrane Systems. Chem Phys Lett. 2013 Jan 03; 555:274-281. Botello-Smith WM, Liu X, Cai Q, Li Z, Zhao H, Luo R. PMID: 23439886; PMCID: PMC3579545.
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    84. Dielectric pressure in continuum electrostatic solvation of biomolecules. Phys Chem Chem Phys. 2012 Dec 05; 14(45):15917-25. Cai Q, Ye X, Luo R. PMID: 23093365; PMCID: PMC5125625.
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    85. Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations. PLoS One. 2012; 7(8):e43788. Ye W, Qin F, Zhang J, Luo R, Chen HF. PMID: 22952765; PMCID: PMC3428290.
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    86. 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. Wang J, Cieplak P, Cai Q, Hsieh MJ, Wang J, Duan Y, Luo R. PMID: 22712654; PMCID: PMC3493849.
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    87. Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations. J Chem Theory Comput. 2012 Aug 14; 8(8):2741-2751. Wang J, Cai Q, Xiang Y, Luo R. PMID: 23185142; PMCID: PMC3505068.
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    88. Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization. J Phys Chem B. 2012 Jun 21; 116(24):7088-101. Wang J, Cieplak P, Li J, Cai Q, Hsieh MJ, Luo R, Duan Y. PMID: 22612331; PMCID: PMC3391542.
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    89. On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods. J Chem Theory Comput. 2011 Nov 01; 7(11):3608-3619. Cai Q, Ye X, Wang J, Luo R. PMID: 24772042; PMCID: PMC3998210.
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    90. Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies. Chem Phys Lett. 2011 Oct; 514(4-6):368-373. Cai Q, Ye X, Wang J, Luo R. PMID: 22125339; PMCID: PMC3224087.
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    91. Virtual screening using molecular simulations. Proteins. 2011 Jun; 79(6):1940-51. Yang T, Wu JC, Yan C, Wang Y, Luo R, Gonzales MB, Dalby KN, Ren P. PMID: 21491494; PMCID: PMC3092865.
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    92. 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. Wang J, Cieplak P, Li J, Wang J, Cai Q, Hsieh M, Lei H, Luo R, Duan Y. PMID: 21391583; PMCID: PMC3082585.
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    93. Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability. J Phys Chem B. 2011 Mar 31; 115(12):3091-9. Wang J, Cieplak P, Li J, Hou T, Luo R, Duan Y. PMID: 21391553; PMCID: PMC3082581.
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    94. Exploring a coarse-grained distributive strategy for finite-difference Poisson-Boltzmann calculations. J Mol Model. 2011 Aug; 17(8):1985-96. Hsieh MJ, Luo R. PMID: 21127924; PMCID: PMC3143316.
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    95. Assessment of linear finite-difference Poisson-Boltzmann solvers. J Comput Chem. 2010 Jun; 31(8):1689-98. Wang J, Luo R. PMID: 20063271; PMCID: PMC2854862.
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    96. A revised density function for molecular surface definition in continuum solvent models. J Chem Theory Comput. 2010 Apr 13; 6(4):1157-1169. Ye X, Wang J, Luo R. PMID: 24723844; PMCID: PMC3979486.
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    97. Balancing simulation accuracy and efficiency with the Amber united atom force field. J Phys Chem B. 2010 Mar 04; 114(8):2886-93. Hsieh MJ, Luo R. PMID: 20131885.
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    98. Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers. J Chem Theory Comput. 2010 Jan 12; 6(1):203-211. Cai Q, Hsieh MJ, Wang J, Luo R. PMID: 24723843; PMCID: PMC3979552.
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    99. Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics. Phys Chem Chem Phys. 2010 Feb 07; 12(5):1194-202. Wang J, Tan C, Chanco E, Luo R. PMID: 20094685.
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    100. Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations. Biophys Chem. 2009 Nov; 145(1):37-44. Tan YH, Chen YM, Ye X, Lu Q, Tretyachenko-Ladokhina V, Yang W, Senear DF, Luo R. PMID: 19748724; PMCID: PMC2794655.
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    101. 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. Ye X, Cai Q, Yang W, Luo R. PMID: 19619470; PMCID: PMC2711334.
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    102. Structural and functional implications of p53 missense cancer mutations. PMC Biophys. 2009 Jun 26; 2(1):5. Tan Y, Luo R. PMID: 19558684; PMCID: PMC2709103.
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    103. On removal of charge singularity in Poisson-Boltzmann equation. J Chem Phys. 2009 Apr 14; 130(14):145101. Cai Q, Wang J, Zhao HK, Luo R. PMID: 19368474.
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    104. 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. Wang J, Cai Q, Li ZL, Zhao HK, Luo R. PMID: 20098487; PMCID: PMC2663913.
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    105. All-atom computer simulations of amyloid fibrils disaggregation. Biophys J. 2008 Dec; 95(11):5037-47. Wang J, Tan C, Chen HF, Luo R. PMID: 18757563; PMCID: PMC2586582.
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    106. Continuum polarizable force field within the Poisson-Boltzmann framework. J Phys Chem B. 2008 Jun 26; 112(25):7675-88. Tan YH, Tan C, Wang J, Luo R. PMID: 18507452; PMCID: PMC2495006.
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    107. 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. Tu C, Tan YH, Shaw G, Zhou Z, Bai Y, Luo R, Ji X. PMID: 18453682; PMCID: PMC2631104.
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    108. Protein stability prediction: a Poisson-Boltzmann approach. J Phys Chem B. 2008 Feb 14; 112(6):1875-83. Tan YH, Luo R. PMID: 18211063.
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    109. Inhibition kinetics and emodin cocrystal structure of a type II polyketide ketoreductase. Biochemistry. 2008 Feb 19; 47(7):1837-47. Korman TP, Tan YH, Wong J, Luo R, Tsai SC. PMID: 18205400; PMCID: PMC2263082.
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    110. Implicit nonpolar solvent models. J Phys Chem B. 2007 Oct 25; 111(42):12263-74. Tan C, Tan YH, Luo R. PMID: 17918880.
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    111. Molecular dynamics simulations of p53 DNA-binding domain. J Phys Chem B. 2007 Oct 04; 111(39):11538-45. Lu Q, Tan YH, Luo R. PMID: 17824689; PMCID: PMC2522240.
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    112. Continuum treatment of electronic polarization effect. J Chem Phys. 2007 Mar 07; 126(9):094103. Tan YH, Luo R. PMID: 17362100.
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    113. Binding induced folding in p53-MDM2 complex. J Am Chem Soc. 2007 Mar 14; 129(10):2930-7. Chen HF, Luo R. PMID: 17302414; PMCID: PMC2528056.
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    114. Force field influences in beta-hairpin folding simulations. Protein Sci. 2006 Nov; 15(11):2642-55. Lwin TZ, Luo R. PMID: 17075138; PMCID: PMC2242415.
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    115. 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. Tan C, Yang L, Luo R. PMID: 16970499.
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    116. New-generation amber united-atom force field. J Phys Chem B. 2006 Jul 06; 110(26):13166-76. Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R. PMID: 16805629.
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    117. 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. 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. PMID: 17048398; PMCID: PMC2748235.
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    118. Is Poisson-Boltzmann theory insufficient for protein folding simulations? J Chem Phys. 2006 Jan 21; 124(3):034902. Lwin TZ, Zhou R, Luo R. PMID: 16438609.
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    119. The Amber biomolecular simulation programs. J Comput Chem. 2005 Dec; 26(16):1668-88. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. PMID: 16200636; PMCID: PMC1989667.
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    120. Overcoming entropic barrier with coupled sampling at dual resolutions. J Chem Phys. 2005 Nov 15; 123(19):194904. Lwin TZ, Luo R. PMID: 16321110.
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    121. 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. Hsieh MJ, Luo R. PMID: 15229881.
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    122. Interplay of secondary structures and side-chain contacts in the denatured state of BBA1. J Chem Phys. 2004 Aug 01; 121(5):2412-21. Wen EZ, Luo R. PMID: 15260796.
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    123. 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. Wen EZ, Hsieh MJ, Kollman PA, Luo R. PMID: 15099837.
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    124. 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. 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. PMID: 14531054.
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    125. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem. 2002 Oct; 23(13):1244-53. Luo R, David L, Gilson MK. PMID: 12210150.
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