Ray Luo - Publications

Affiliations: 
University of California, Los Angeles, Los Angeles, CA 
Area:
Computational Neuroscience, Synaptic Physiology, fMRI, Computer Vision, Motor Control
Website:
http://rayluo.bol.ucla.edu/projects/

82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Aspacio D, Zhang Y, Cui Y, Luu E, King E, Black WB, Perea S, Zhu Q, Wu Y, Luo R, Siegel JB, Li H. Shifting redox reaction equilibria on demand using an orthogonal redox cofactor. Nature Chemical Biology. PMID 39138383 DOI: 10.1038/s41589-024-01702-5  0.334
2024 Rehman AU, Zhao C, Wu Y, Zhu Q, Luo R. Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy. International Journal of Molecular Sciences. 25. PMID 38892388 DOI: 10.3390/ijms25116201  0.372
2024 Zhu Q, Wu Y, Luo R. Understanding and fine tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine. Physical Chemistry Chemical Physics : Pccp. 26: 10568-10578. PMID 38512104 DOI: 10.1039/d4cp00761a  0.376
2023 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, ... ... Luo R, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153  0.337
2023 Wu Y, Wei H, Zhu Q, Luo R. Grid-Robust Efficient Neural Interface Model for Universal Molecule Surface Construction from Point Clouds. The Journal of Physical Chemistry Letters. 14: 9034-9041. PMID 37782231 DOI: 10.1021/acs.jpclett.3c02176  0.391
2023 Zhu Q, Wu Y, Zhao S, Cieplak P, Duan Y, Luo R. Streamlining and Optimizing Strategies of Electrostatic Parameterization. Journal of Chemical Theory and Computation. PMID 37676646 DOI: 10.1021/acs.jctc.3c00659  0.418
2023 Zhu Q, Luo R. Recent Advances in Biomolecular Recognition. International Journal of Molecular Sciences. 24. PMID 37176015 DOI: 10.3390/ijms24098310  0.324
2020 Wei H, Qi R, Wang J, Cieplak P, Duan Y, Luo R. Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations. The Journal of Chemical Physics. 153: 114116. PMID 32962395 DOI: 10.1063/5.0019560  0.388
2020 Song D, Liu H, Luo R, Chen HF. Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. Journal of Chemical Information and Modeling. PMID 32227937 DOI: 10.1021/Acs.Jcim.0C00059  0.338
2019 Zhang Y, Liu H, Yang S, Luo R, Chen HF. A Well-Balanced Force Field ff03CMAP for Folded and Disordered Proteins. Journal of Chemical Theory and Computation. PMID 31657215 DOI: 10.1021/Acs.Jctc.9B00623  0.321
2019 Liu H, Song D, Zhang Y, Yang S, Luo R, Chen HF. Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins. Physical Chemistry Chemical Physics : Pccp. PMID 31552948 DOI: 10.1039/C9Cp03434J  0.325
2019 Wei H, Luo A, Qiu T, Luo R, Qi R. Improved Poisson-Boltzmann Methods for High-Performance Computing. Journal of Chemical Theory and Computation. PMID 31525962 DOI: 10.1021/Acs.Jctc.9B00602  0.337
2019 Greene D, Qi R, Nguyen R, Qiu T, Luo R. A Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. Journal of Chemical Information and Modeling. PMID 31145610 DOI: 10.1021/Acs.Jcim.9B00363  0.313
2019 Wei H, Luo R, Qi R. An efficient second-order poisson-boltzmann method. Journal of Computational Chemistry. PMID 30776135 DOI: 10.1002/Jcc.25783  0.336
2019 Wang J, Cieplak P, Luo R, Duan Y. Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization to Reproduce Ab Initio Anisotropy. Journal of Chemical Theory and Computation. PMID 30645118 DOI: 10.1021/Acs.Jctc.8B00603  0.341
2018 Qi R, Luo R. Robustness and Efficiency of Poisson-Boltzmann Modeling on GPUs. Journal of Chemical Information and Modeling. PMID 30550277 DOI: 10.1021/Acs.Jcim.8B00761  0.332
2018 Duong VT, Chen Z, Thapa MT, Luo R. Computational Studies of Intrinsically Disordered Proteins. The Journal of Physical Chemistry. B. PMID 30372613 DOI: 10.1021/Acs.Jpcb.8B09029  0.344
2018 Liu H, Song D, Lu H, Luo R, Chen HF. Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF. Chemical Biology & Drug Design. PMID 29808548 DOI: 10.1111/Cbdd.13342  0.34
2018 Ellis BD, Milligan JC, White AR, Duong V, Altman PX, Mohammed L, Crump MP, Crosby J, Luo R, Vanderwal CD, Tsai SC. An Oxetane-based Polyketide Surrogate to Probe Substrate Binding in a Polyketide Synthase. Journal of the American Chemical Society. PMID 29620883 DOI: 10.1021/Jacs.7B11793  0.304
2018 Duong VT, Thapa M, Luo R. Improved Accuracy and Convergence of Intrinsically Disordered Protein Molecular Dynamics Simulations Using the ff14IDPSFF Force Field Biophysical Journal. 114: 432a. DOI: 10.1016/J.Bpj.2017.11.2394  0.324
2017 Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Frontiers in Molecular Biosciences. 4: 87. PMID 29367919 DOI: 10.3389/Fmolb.2017.00087  0.348
2017 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. The Journal of Chemical Physics. 147: 214112. PMID 29221408 DOI: 10.1063/1.5016052  0.339
2017 Wang C, Ren P, Luo R. Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling. The Journal of Physical Chemistry. B. PMID 29164898 DOI: 10.1021/Acs.Jpcb.7B09616  0.369
2017 Guo X, Han J, Luo R, Chen HF. Conformation Dynamics of the Intrinsically Disordered Protein c-Myb with the ff99IDPs Force Field. Rsc Advances. 7: 29713-29721. PMID 29104751 DOI: 10.1039/C7Ra04133K  0.308
2017 Qi R, Botello-Smith WM, Luo R. Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units. Journal of Chemical Theory and Computation. PMID 28553983 DOI: 10.1021/Acs.Jctc.7B00336  0.34
2017 Song D, Luo R, Chen HF. IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling. PMID 28448138 DOI: 10.1021/Acs.Jcim.7B00135  0.365
2017 Ye W, Qian T, Liu H, Luo R, Chen HF. Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. Journal of Chemical Information and Modeling. PMID 28425706 DOI: 10.1021/Acs.Jcim.7B00073  0.308
2017 Wang C, Xiao L, Luo R. Numerical interpretation of molecular surface field in dielectric modeling of solvation. Journal of Computational Chemistry. PMID 28318096 DOI: 10.1002/Jcc.24782  0.381
2016 Greene D, Botello-Smith WM, Follmer A, Xiao L, Lambros E, Luo R. Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor. The Journal of Physical Chemistry. B. 120: 12293-12304. PMID 27934233 DOI: 10.1021/Acs.Jpcb.6B09535  0.324
2016 Wang C, Nguyen PH, Pham K, Huynh D, Le TN, Wang H, Ren P, Luo R. Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. Journal of Computational Chemistry. PMID 27510546 DOI: 10.1002/Jcc.24467  0.358
2016 Song D, Wang W, Ye W, Ji D, Luo R, Chen HF. ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins. Chemical Biology & Drug Design. PMID 27484738 DOI: 10.1111/Cbdd.12832  0.344
2015 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. Journal of Computational Physics. 297: 182-193. PMID 27087702 DOI: 10.1016/J.Jcp.2015.05.003  0.31
2015 Botello-Smith WM, Luo R. Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation. Journal of Chemical Information and Modeling. 55: 2187-99. PMID 26389966 DOI: 10.1021/Acs.Jcim.5B00341  0.342
2015 Ye W, Ji D, Wang W, Luo R, Chen HF. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling. 55: 1021-9. PMID 25919886 DOI: 10.1021/Acs.Jcim.5B00043  0.329
2014 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. Chemical Physics Letters. 616: 67-74. PMID 25404761 DOI: 10.1016/J.Cplett.2014.10.033  0.302
2014 Wang W, Ye W, Jiang C, Luo R, Chen HF. New force field on modeling intrinsically disordered proteins. Chemical Biology & Drug Design. 84: 253-69. PMID 24589355 DOI: 10.1111/Cbdd.12314  0.322
2014 Botello-Smith WM, Cai Q, Luo R. Biological applications of classical electrostatics methods Journal of Theoretical and Computational Chemistry. 13: 1440008. DOI: 10.1142/S0219633614400082  0.323
2014 Xiao L, Wang C, Luo R. Recent progress in adapting Poisson–Boltzmann methods to molecular simulations Journal of Theoretical and Computational Chemistry. 13: 1430001. DOI: 10.1142/S0219633614300018  0.359
2013 Wang C, Wang J, Cai Q, Li Z, Zhao HK, Luo R. Exploring accurate Poisson-Boltzmann methods for biomolecular simulations. Computational & Theoretical Chemistry. 1024: 34-44. PMID 24443709 DOI: 10.1016/J.Comptc.2013.09.021  0.345
2013 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. Physical Chemistry Chemical Physics : Pccp. 15: 18510-22. PMID 24072031 DOI: 10.1039/C3Cp53145G  0.348
2013 Xiao L, Cai Q, Ye X, Wang J, Luo R. Electrostatic forces in the Poisson-Boltzmann systems. The Journal of Chemical Physics. 139: 094106. PMID 24028101 DOI: 10.1063/1.4819471  0.33
2013 Botello-Smith WM, Liu X, Cai Q, Li Z, Zhao H, Luo R. Numerical Poisson-Boltzmann Model for Continuum Membrane Systems. Chemical Physics Letters. 555: 274-281. PMID 23439886 DOI: 10.1016/J.Cplett.2012.10.081  0.335
2013 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. Physical Chemistry Chemical Physics : Pccp. 15: 129-41. PMID 23147243 DOI: 10.1039/C2Cp41894K  0.31
2012 Wang J, Cai Q, Xiang Y, Luo R. Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations. Journal of Chemical Theory and Computation. 8: 2741-2751. PMID 23185142 DOI: 10.1021/Ct300341D  0.341
2012 Cai Q, Ye X, Luo R. Dielectric pressure in continuum electrostatic solvation of biomolecules. Physical Chemistry Chemical Physics : Pccp. 14: 15917-25. PMID 23093365 DOI: 10.1039/C2Cp43237D  0.347
2012 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. The Journal of Physical Chemistry. B. 116: 7999-8008. PMID 22712654 DOI: 10.1021/Jp212117D  0.303
2012 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. The Journal of Physical Chemistry. B. 116: 7088-101. PMID 22612331 DOI: 10.1021/Jp3019759  0.324
2012 Dellal SS, Luo R, Otis TS. GABAA receptors increase excitability and conduction velocity of cerebellar parallel fiber axons. Journal of Neurophysiology. 107: 2958-70. PMID 22378171 DOI: 10.1152/jn.01028.2011  0.602
2012 Cai Q, Wang J, Hsieh M, Ye X, Luo R. Chapter Six - Poisson–Boltzmann Implicit Solvation Models Annual Reports in Computational Chemistry. 8: 149-162. DOI: 10.1016/B978-0-444-59440-2.00006-5  0.398
2011 Cai Q, Ye X, Wang J, Luo R. On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods. Journal of Chemical Theory and Computation. 7: 3608-3619. PMID 24772042 DOI: 10.1021/Ct200389P  0.322
2011 Cai Q, Ye X, Wang J, Luo R. Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies. Chemical Physics Letters. 514: 368-373. PMID 22125339 DOI: 10.1016/J.Cplett.2011.08.067  0.35
2011 Yang T, Wu JC, Yan C, Wang Y, Luo R, Gonzales MB, Dalby KN, Ren P. Virtual screening using molecular simulations. Proteins. 79: 1940-51. PMID 21491494 DOI: 10.1002/Prot.23018  0.35
2011 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. The Journal of Physical Chemistry. B. 115: 3100-11. PMID 21391583 DOI: 10.1021/Jp1121382  0.331
2011 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. The Journal of Physical Chemistry. B. 115: 3091-9. PMID 21391553 DOI: 10.1021/Jp112133G  0.32
2011 Hsieh MJ, Luo R. Exploring a coarse-grained distributive strategy for finite-difference Poisson-Boltzmann calculations. Journal of Molecular Modeling. 17: 1985-96. PMID 21127924 DOI: 10.1007/S00894-010-0904-4  0.317
2010 Ye X, Wang J, Luo R. A revised density function for molecular surface definition in continuum solvent models. Journal of Chemical Theory and Computation. 6: 1157-1169. PMID 24723844 DOI: 10.1021/Ct900318U  0.331
2010 Hsieh MJ, Luo R. Balancing simulation accuracy and efficiency with the Amber united atom force field. The Journal of Physical Chemistry. B. 114: 2886-93. PMID 20131885 DOI: 10.1021/Jp906701S  0.317
2010 Wang J, Tan C, Chanco E, Luo R. Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics. Physical Chemistry Chemical Physics : Pccp. 12: 1194-202. PMID 20094685 DOI: 10.1039/B917775B  0.354
2009 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. Chemical Physics Letters. 468: 112-118. PMID 20098487 DOI: 10.1016/J.Cplett.2008.12.049  0.356
2009 Bradley J, Luo R, Otis TS, DiGregorio DA. Submillisecond optical reporting of membrane potential in situ using a neuronal tracer dye. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 29: 9197-209. PMID 19625510 DOI: 10.1523/Jneurosci.1240-09.2009  0.563
2009 Cai Q, Wang J, Zhao HK, Luo R. On removal of charge singularity in Poisson-Boltzmann equation. The Journal of Chemical Physics. 130: 145101. PMID 19368474 DOI: 10.1063/1.3099708  0.353
2008 Tan YH, Tan C, Wang J, Luo R. Continuum polarizable force field within the Poisson-Boltzmann framework. The Journal of Physical Chemistry. B. 112: 7675-88. PMID 18507452 DOI: 10.1021/Jp7110988  0.345
2007 Tan C, Tan YH, Luo R. Implicit nonpolar solvent models. The Journal of Physical Chemistry. B. 111: 12263-74. PMID 17918880 DOI: 10.1021/Jp073399N  0.315
2007 Tan YH, Luo R. Continuum treatment of electronic polarization effect. The Journal of Chemical Physics. 126: 094103. PMID 17362100 DOI: 10.1063/1.2436871  0.313
2006 Lwin TZ, Luo R. Force field influences in beta-hairpin folding simulations. Protein Science : a Publication of the Protein Society. 15: 2642-55. PMID 17075138 DOI: 10.1110/Ps.062438006  0.342
2006 Tan C, Yang L, Luo R. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis. The Journal of Physical Chemistry. B. 110: 18680-7. PMID 16970499 DOI: 10.1021/Jp063479B  0.301
2006 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. The Journal of Physical Chemistry. B. 110: 13166-76. PMID 16805629 DOI: 10.1021/Jp060163V  0.32
2006 Lwin TZ, Zhou R, Luo R. Is Poisson-Boltzmann theory insufficient for protein folding simulations? The Journal of Chemical Physics. 124: 034902. PMID 16438609 DOI: 10.1063/1.2161202  0.334
2005 Lwin TZ, Luo R. Overcoming entropic barrier with coupled sampling at dual resolutions. The Journal of Chemical Physics. 123: 194904. PMID 16321110 DOI: 10.1063/1.2102871  0.36
2004 Hsieh MJ, Luo R. Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction. Proteins. 56: 475-86. PMID 15229881 DOI: 10.1002/Prot.20133  0.324
2004 Wen EZ, Hsieh MJ, Kollman PA, Luo R. Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces. Journal of Molecular Graphics & Modelling. 22: 415-24. PMID 15099837 DOI: 10.1016/J.Jmgm.2003.12.008  0.34
2003 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. Journal of Computational Chemistry. 24: 1999-2012. PMID 14531054 DOI: 10.1002/Jcc.10349  0.355
2002 Luo R, David L, Gilson MK. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. Journal of Computational Chemistry. 23: 1244-53. PMID 12210150 DOI: 10.1002/Jcc.10120  0.582
2001 Wang W, Lim WA, Jakalian A, Wang J, Wang J, Luo R, Bayly CI, Kollman PA. 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. 123: 3986-94. PMID 11457149 DOI: 10.1021/Ja003164O  0.352
2001 Mardis KL, Luo R, Gilson MK. Interpreting trends in the binding of cyclic ureas to HIV-1 protease Journal of Molecular Biology. 309: 507-517. PMID 11371168 DOI: 10.1006/Jmbi.2001.4668  0.548
2001 David L, Luo R, Gilson MK. Ligand-receptor docking with the Mining Minima optimizer Journal of Computer-Aided Molecular Design. 15: 157-171. PMID 11272702 DOI: 10.1023/A:1008128723048  0.545
2001 Luo R, Gilson HSR, Potter MJ, Gilson MK. The physical basis of nucleic acid base stacking in water Biophysical Journal. 80: 140-148. PMID 11159389 DOI: 10.1016/S0006-3495(01)76001-8  0.522
2000 Mardis K, Luo R, David L, Potter M, Glemza A, Payne G, Gilson MK. Modeling molecular recognition: Theory and application Journal of Biomolecular Structure and Dynamics. 17: 89-94. DOI: 10.1080/07391102.2000.10506608  0.573
2000 David L, Luo R, Gilson MK. Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease Journal of Computational Chemistry. 21: 295-309. DOI: 10.1002/(Sici)1096-987X(200003)21:4<295::Aid-Jcc5>3.0.Co;2-8  0.502
1999 Luo R, Head MS, Given JA, Gilson MK. Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: Affinity and conformation Biophysical Chemistry. 78: 183-193. PMID 10343387 DOI: 10.1016/S0301-4622(98)00229-4  0.554
1999 David L, Luo R, Head MS, Gilson MK. Computational Study Of Kni-272, A Potent Inhibitor Of Hiv-1 Protease : On The Mechanism Of Preorganization Journal of Physical Chemistry B. 103: 1031-1044. DOI: 10.1021/Jp983675L  0.535
1999 Luo R, David L, Hung H, Devaney aJ, Gilson MK. Strength of Solvent-Exposed Salt-Bridges† The Journal of Physical Chemistry. 103: 727-736. DOI: 10.1021/Jp982715I  0.553
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