| Year |
Citation |
Score |
| 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 |
0.339 |
|
| 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 |
0.322 |
|
| 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 |
0.326 |
|
| 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 |
0.315 |
|
| 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 |
0.335 |
|
| 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 |
0.34 |
|
| 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 |
0.331 |
|
| 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 |
0.341 |
|
| 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 |
0.326 |
|
| 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 |
0.347 |
|
| 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 |
0.338 |
|
| 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 |
0.309 |
|
| 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 |
0.337 |
|
| 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 |
0.382 |
|
| 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 |
0.325 |
|
| 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 |
0.345 |
|
| 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 |
0.312 |
|
| 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 |
0.343 |
|
| 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 |
0.331 |
|
| 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 |
0.321 |
|
| 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 |
0.32 |
|
| 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 |
0.36 |
|
| 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 |
0.346 |
|
| 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 |
0.347 |
|
| 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 |
0.333 |
|
| 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 |
0.343 |
|
| 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 |
0.348 |
|
| 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 |
0.322 |
|
| 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 |
0.592 |
|
| 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 |
0.399 |
|
| 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 |
0.351 |
|
| 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 |
0.349 |
|
| 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 |
0.33 |
|
| 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 |
0.319 |
|
| 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 |
0.316 |
|
| 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 |
0.332 |
|
| 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 |
0.318 |
|
| 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 |
0.359 |
|
| 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 |
0.355 |
|
| 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 |
0.347 |
|
| 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 |
0.344 |
|
| 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 |
0.302 |
|
| 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 |
0.322 |
|
| 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 |
0.332 |
|
| 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 |
0.361 |
|
| 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 |
0.583 |
|
| 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 |
0.354 |
|
| 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 |
0.549 |
|
| 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 |
0.546 |
|
| 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 |
0.523 |
|
| 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 |
0.572 |
|
| 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 |
0.503 |
|
| 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 |
0.553 |
|
| 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 |
0.537 |
|
| 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 |
0.555 |
|
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