| 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 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2016 |
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. The Journal of Physical Chemistry. B. PMID 27146097 DOI: 10.1021/Acs.Jpcb.6B04439 |
0.3 |
|
| 2003 |
Lu Q, Luo R. A Poisson-Boltzmann dynamics method with nonperiodic boundary condition Journal of Chemical Physics. 119: 11035-11047. DOI: 10.1063/1.1622376 |
0.3 |
|
| 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 |
0.299 |
|
| 2013 |
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. The Journal of Physical Chemistry. B. 117: 4912-23. PMID 23548180 DOI: 10.1021/Jp4010967 |
0.298 |
|
| 2018 |
Liu H, Guo X, Han J, Luo R, Chen HF. Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB. The Journal of Chemical Physics. 148: 225101. PMID 29907037 DOI: 10.1063/1.5027869 |
0.295 |
|
| 2010 |
Cai Q, Hsieh MJ, Wang J, Luo R. Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers. Journal of Chemical Theory and Computation. 6: 203-211. PMID 24723843 DOI: 10.1021/Ct900381R |
0.292 |
|
| 2007 |
Chen HF, Luo R. Binding induced folding in p53-MDM2 complex. Journal of the American Chemical Society. 129: 2930-7. PMID 17302414 DOI: 10.1021/Ja0678774 |
0.292 |
|
| 2008 |
Tan YH, Luo R. Protein stability prediction: a Poisson-Boltzmann approach. The Journal of Physical Chemistry. B. 112: 1875-83. PMID 18211063 DOI: 10.1021/Jp709660V |
0.291 |
|
| 2007 |
Lu Q, Tan YH, Luo R. Molecular dynamics simulations of p53 DNA-binding domain. The Journal of Physical Chemistry. B. 111: 11538-45. PMID 17824689 DOI: 10.1021/Jp0742261 |
0.291 |
|
| 2014 |
Yu Q, Ye W, Jiang C, Luo R, Chen HF. Specific recognition mechanism between RNA and the KH3 domain of Nova-2 protein. The Journal of Physical Chemistry. B. 118: 12426-34. PMID 25300025 DOI: 10.1021/Jp5079289 |
0.289 |
|
| 2019 |
Schaub AJ, Moreno GO, Zhao S, Truong HV, Luo R, Tsai SC. Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases. Methods in Enzymology. 622: 375-409. PMID 31155062 DOI: 10.1016/Bs.Mie.2019.03.001 |
0.289 |
|
| 2019 |
Milligan JC, Lee DJ, Jackson DR, Schaub AJ, Beld J, Barajas JF, Hale JJ, Luo R, Burkart MD, Tsai SC. Molecular basis for interactions between an acyl carrier protein and a ketosynthase. Nature Chemical Biology. PMID 31209348 DOI: 10.1038/S41589-019-0301-Y |
0.289 |
|
| 2017 |
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. Scientific Reports. 7: 40254. PMID 28074848 DOI: 10.1038/Srep40254 |
0.287 |
|
| 2004 |
Wen EZ, Luo R. Interplay of secondary structures and side-chain contacts in the denatured state of BBA1. The Journal of Chemical Physics. 121: 2412-21. PMID 15260796 DOI: 10.1063/1.1768151 |
0.285 |
|
| 2016 |
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. Journal of Chemical Information and Modeling. PMID 27227511 DOI: 10.1021/Acs.Jcim.6B00115 |
0.283 |
|
| 2015 |
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. Chemistry & Biology. PMID 26235055 DOI: 10.1016/J.Chembiol.2015.06.022 |
0.283 |
|
| 2019 |
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, et al. Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor. The Embo Journal. e102406. PMID 31782549 DOI: 10.15252/Embj.2019102406 |
0.283 |
|
| 2008 |
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 Crystallographica. Section D, Biological Crystallography. 64: 471-7. PMID 18453682 DOI: 10.1107/S0907444908003338 |
0.281 |
|
| 2017 |
Xiao L, Diao J, Greene D, Wang J, Luo R. A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins. Journal of Chemical Theory and Computation. PMID 28564540 DOI: 10.1021/Acs.Jctc.7B00382 |
0.281 |
|
| 2018 |
Greene D, Po T, Pan J, Tabibian T, Luo R. Computational Analysis for the Rational Design of Anti-Amyloid Beta (A β) Antibodies. The Journal of Physical Chemistry. B. PMID 29617557 DOI: 10.1021/Acs.Jpcb.8B01837 |
0.279 |
|
| 2005 |
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. Journal of Computational Chemistry. 26: 1668-88. PMID 16200636 DOI: 10.1002/Jcc.20290 |
0.279 |
|
| 2017 |
Guo X, Han J, Luo R, Chen H. Correction: Conformation dynamics of the intrinsically disordered protein c-Myb with the ff99IDPs force field Rsc Advances. 7: 32093-32093. DOI: 10.1039/C7Ra90072D |
0.278 |
|
| 2012 |
Ye W, Qin F, Zhang J, Luo R, Chen HF. Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations. Plos One. 7: e43788. PMID 22952765 DOI: 10.1371/Journal.Pone.0043788 |
0.277 |
|
| 2009 |
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. Biophysical Chemistry. 145: 37-44. PMID 19748724 DOI: 10.1016/J.Bpc.2009.08.008 |
0.276 |
|
| 2008 |
Wang J, Tan C, Chen HF, Luo R. All-atom computer simulations of amyloid fibrils disaggregation. Biophysical Journal. 95: 5037-47. PMID 18757563 DOI: 10.1529/Biophysj.108.131672 |
0.273 |
|
| 2018 |
Zhang L, King E, Luo R, Li H. Development of a high-throughput, in vivo selection platform for NADPH-dependent reactions based on redox balance principles. Acs Synthetic Biology. PMID 29939709 DOI: 10.1021/Acssynbio.8B00179 |
0.27 |
|
| 2016 |
Wang W, Jiang C, Zhang J, Ye W, Luo R, Chen HF. Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Scientific Reports. 6: 31005. PMID 27484311 DOI: 10.1038/Srep31005 |
0.263 |
|
| 2015 |
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. The Journal of Physical Chemistry. B. 119: 2844-56. PMID 25633018 DOI: 10.1021/Jp510940W |
0.263 |
|
| 2010 |
Li CZ, Koter M, Ye X, Zhou SF, Chou W, Luo R, Gershon PD. Widespread but small-scale changes in the structural and dynamic properties of vaccinia virus poly(A) polymerase upon association with its processivity factor in solution. Biochemistry. 49: 6247-62. PMID 20469877 DOI: 10.1021/Bi100166X |
0.262 |
|
| 2009 |
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. Biophysical Journal. 97: 554-62. PMID 19619470 DOI: 10.1016/J.Bpj.2009.05.012 |
0.259 |
|
| 2019 |
Li Q, Luo R, Chen HF. Dynamical Important Residue Network (DIRN): Network Inference via Conformational Change. Bioinformatics (Oxford, England). PMID 31038692 DOI: 10.1093/Bioinformatics/Btz298 |
0.253 |
|
| 2016 |
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. Scientific Reports. 6: 24587. PMID 27079666 DOI: 10.1038/Srep24587 |
0.252 |
|
| 2009 |
Tan Y, Luo R. Structural and functional implications of p53 missense cancer mutations. Pmc Biophysics. 2: 5. PMID 19558684 DOI: 10.1186/1757-5036-2-5 |
0.249 |
|
| 2016 |
Zhang JM, Jiang C, Ye W, Luo R, Chen HF. Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network. Molecular Biosystems. PMID 27841427 DOI: 10.1039/C6Mb00630B |
0.248 |
|
| 2015 |
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 Chemical Biology. PMID 26473393 DOI: 10.1021/Acschembio.5B00500 |
0.247 |
|
| 2021 |
King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery. Frontiers in Molecular Biosciences. 8: 712085. PMID 34458321 DOI: 10.3389/fmolb.2021.712085 |
0.235 |
|
| 2006 |
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 Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 114-25. PMID 17048398 DOI: 10.1109/Tcbb.2006.22 |
0.231 |
|
| 2021 |
Zhao S, Schaub AJ, Tsai SC, Luo R. Development of a Pantetheine Force Field Library for Molecular Modeling. Journal of Chemical Information and Modeling. PMID 33534558 DOI: 10.1021/acs.jcim.0c01384 |
0.231 |
|
| 2018 |
Han H, Qi R, Zhou JJ, Ta AP, Yang B, Nakaoka HJ, Seo G, Guan KL, Luo R, Wang W. Regulation of the Hippo Pathway by Phosphatidic Acid-Mediated Lipid-Protein Interaction. Molecular Cell. PMID 30293781 DOI: 10.1016/J.Molcel.2018.08.038 |
0.229 |
|
| 2021 |
Mu J, Liu H, Zhang J, Luo R, Chen HF. Recent Force Field Strategies for Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling. PMID 33591749 DOI: 10.1021/acs.jcim.0c01175 |
0.228 |
|
| 2021 |
King E, Qi R, Li H, Luo R, Aitchison E. Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. Journal of Chemical Theory and Computation. PMID 33764050 DOI: 10.1021/acs.jctc.0c01305 |
0.224 |
|
| 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 |
0.223 |
|
| 2023 |
Zhao S, Cieplak P, Duan Y, Luo R. Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation. 19: 924-941. PMID 36696564 DOI: 10.1021/acs.jctc.2c01048 |
0.221 |
|
| 2022 |
Zhao S, Wei H, Cieplak P, Duan Y, Luo R. Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation. PMID 36094401 DOI: 10.1021/acs.jctc.2c00710 |
0.219 |
|
| 2022 |
Wei H, Cieplak P, Duan Y, Luo R. Stress tensor and constant pressure simulation for polarizable Gaussian multipole model. The Journal of Chemical Physics. 156: 114114. PMID 35317572 DOI: 10.1063/5.0082548 |
0.216 |
|
| 2020 |
Maxel S, Zhang L, King E, Acosta AP, Luo R, Li H. In Vivo, High-Throughput Selection of Thermostable Cyclohexanone Monooxygenase (CHMO) Catalysts. 10: 935. DOI: 10.3390/Catal10080935 |
0.216 |
|
| 2024 |
Duan Y, Niu T, Wang J, Cieplak P, Luo R. PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents. Journal of Chemical Theory and Computation. PMID 38502776 DOI: 10.1021/acs.jctc.4c00064 |
0.212 |
|
| 2018 |
Black W, King E, Wang Y, Jenic A, Rowley AT, Seki K, Luo R, Li H. Engineering a Coenzyme A detour to expand the product scope and enhance the selectivity of the Ehrlich pathway. Acs Synthetic Biology. PMID 30433765 DOI: 10.1021/Acssynbio.8B00358 |
0.211 |
|
| 2022 |
Zhao S, Wei H, Cieplak P, Duan Y, Luo R. : A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields. Journal of Chemical Theory and Computation. PMID 35537209 DOI: 10.1021/acs.jctc.2c00230 |
0.203 |
|
| 2024 |
Zhao S, Cieplak P, Duan Y, Luo R. Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation. PMID 38394331 DOI: 10.1021/acs.jctc.3c01347 |
0.191 |
|
| 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 |
0.184 |
|
| 2010 |
Wang J, Luo R. Assessment of linear finite-difference Poisson-Boltzmann solvers. Journal of Computational Chemistry. 31: 1689-98. PMID 20063271 DOI: 10.1002/jcc.21456 |
0.184 |
|
| 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 |
0.163 |
|
| 2021 |
Maxel S, Saleh S, King E, Aspacio D, Zhang L, Luo R, Li H. Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst. Acs Synthetic Biology. PMID 34469126 DOI: 10.1021/acssynbio.1c00258 |
0.155 |
|
| 2020 |
Zhao S, Ni F, Qiu T, Wolff JT, Tsai SC, Luo R. Molecular Basis for Polyketide Ketoreductase-Substrate Interactions. International Journal of Molecular Sciences. 21. PMID 33066287 DOI: 10.3390/ijms21207562 |
0.15 |
|
| 2008 |
Korman TP, Tan YH, Wong J, Luo R, Tsai SC. Inhibition kinetics and emodin cocrystal structure of a type II polyketide ketoreductase. Biochemistry. 47: 1837-47. PMID 18205400 DOI: 10.1021/Bi7016427 |
0.148 |
|
| 2020 |
Maxel S, King E, Zhang Y, Luo R, Li H. Leveraging Oxidative Stress to Regulate Redox Balance-Based, In Vivo Growth Selections for Oxygenase Engineering. Acs Synthetic Biology. PMID 32966747 DOI: 10.1021/acssynbio.0c00380 |
0.144 |
|
| 2019 |
Lu SB, Chai H, Ward JS, Quan M, Zhang J, Rissanen K, Luo R, Yang LP, Jiang W. A 2,3-dialkoxynaphthalene-based naphthocage. Chemical Communications (Cambridge, England). PMID 31858093 DOI: 10.1039/C9Cc09585C |
0.139 |
|
| 2021 |
Wei H, Zhao Z, Luo R. Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations. Journal of Chemical Theory and Computation. PMID 34516109 DOI: 10.1021/acs.jctc.1c00492 |
0.139 |
|
| 2022 |
Khurshid B, Rehman AU, Luo R, Khan A, Wadood A, Anwar J. Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations. Acs Omega. 7: 15132-15144. PMID 35572757 DOI: 10.1021/acsomega.2c01034 |
0.135 |
|
| 2023 |
Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opinion On Drug Discovery. PMID 36715303 DOI: 10.1080/17460441.2023.2171396 |
0.131 |
|
| 2022 |
King E, Cui Y, Aspacio D, Nicklen F, Zhang L, Maxel S, Luo R, Siegel JB, Aitchison E, Li H. Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power. Acs Catalysis. 12: 8582-8592. PMID 37622090 DOI: 10.1021/acscatal.2c01837 |
0.126 |
|
| 2020 |
Maxel S, Zhang L, King E, Acosta AP, Luo R, Li H. In Vivo, High-Throughput Selection of Thermostable Cyclohexanone Monooxygenase (CHMO). Catalysts (Basel, Switzerland). 10. PMID 37637965 DOI: 10.3390/catal10080935 |
0.122 |
|
| 2024 |
Shadman H, Ziebarth JD, Gallops CE, Luo R, Li Z, Chen HF, Wang Y. Map Conformational Landscapes of Intrinsically Disordered Proteins with Polymer Physics Quantities. Biophysical Journal. PMID 38615193 DOI: 10.1016/j.bpj.2024.04.010 |
0.12 |
|
| 2022 |
Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H. Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nature Communications. 13: 5021. PMID 36028482 DOI: 10.1038/s41467-022-32727-w |
0.118 |
|
| 2022 |
King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nature Communications. 13: 7282. PMID 36435948 DOI: 10.1038/s41467-022-35021-x |
0.117 |
|
| 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 |
0.109 |
|
| 2023 |
Huang Z, Zhao S, Cieplak P, Duan Y, Luo R, Wei H. Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models. Journal of Chemical Theory and Computation. PMID 37441805 DOI: 10.1021/acs.jctc.3c00226 |
0.108 |
|
| 2022 |
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, et al. Motif-dependent immune co-receptor interactome profiling by photoaffinity chemical proteomics. Cell Chemical Biology. PMID 35093210 DOI: 10.1016/j.chembiol.2022.01.005 |
0.099 |
|
| 2023 |
Zhu Q, Luo R. Recent Advances in Biomolecular Recognition. International Journal of Molecular Sciences. 24. PMID 37176015 DOI: 10.3390/ijms24098310 |
0.094 |
|
| 2023 |
Ji H, Lu X, Zhao S, Wang Q, Liao B, Bauer LG, Huber KVM, Luo R, Tian R, Tan CSH. Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions. Cell Chemical Biology. PMID 37652024 DOI: 10.1016/j.chembiol.2023.08.002 |
0.082 |
|
| 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. DOI: 10.1016/j.jcp.2015.05.003 |
0.069 |
|
| 2023 |
Ain Nazir NU, Shaukat MH, Luo R, Abbas SR. Novel breath biomarkers identification for early detection of hepatocellular carcinoma and cirrhosis using ML tools and GCMS. Plos One. 18: e0287465. PMID 37967076 DOI: 10.1371/journal.pone.0287465 |
0.055 |
|
| 2018 |
Luo R, Uematsu A, Weitemier A, Aquili L, Koivumaa J, McHugh TJ, Johansen JP. A dopaminergic switch for fear to safety transitions. Nature Communications. 9: 2483. PMID 29950562 DOI: 10.1038/S41467-018-04784-7 |
0.047 |
|
| 2022 |
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, et al. The Hippo pathway kinases LATS1 and LATS2 attenuate cellular responses to heavy metals through phosphorylating MTF1. Nature Cell Biology. 24: 74-87. PMID 35027733 DOI: 10.1038/s41556-021-00813-8 |
0.042 |
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