Pengyu Ren - Publications

Affiliations: 
2015- Biomedical Engineering University of Texas at Austin, Austin, Texas, U.S.A. 

119 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
2022 Walker B, Liu C, Wait E, Ren P. Automation of AMOEBA polarizable force field for small molecules: Poltype 2. Journal of Computational Chemistry. PMID 35778723 DOI: 10.1002/jcc.26954  0.562
2022 Arabzadeh H, Liu C, Acevedo O, Ren P, Yang W, Albrecht-Schönzart T. Hydration of divalent lanthanides, Sm and Eu : A molecular dynamics study with polarizable AMOEBA force field. Journal of Computational Chemistry. PMID 35648124 DOI: 10.1002/jcc.26933  0.54
2022 Naseem-Khan S, Lagardère L, Narth C, Cisneros GA, Ren P, Gresh N, Piquemal JP. Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 35575306 DOI: 10.1021/acs.jctc.2c00029  0.359
2022 El Khoury L, Jing Z, Cuzzolin A, Deplano A, Loco D, Sattarov B, Hédin F, Wendeborn S, Ho C, El Ahdab D, Jaffrelot Inizan T, Sturlese M, Sosic A, Volpiana M, Lugato A, ... ... Ren P, et al. Computationally driven discovery of SARS-CoV-2 M inhibitors: from design to experimental validation. Chemical Science. 13: 3674-3687. PMID 35432906 DOI: 10.1039/d1sc05892d  0.73
2022 Yang X, Liu C, Walker BD, Ren P. Accurate description of molecular dipole surface with charge flux implemented for molecular mechanics. The Journal of Chemical Physics. 153: 064103. PMID 35287459 DOI: 10.1063/5.0016376  0.711
2021 Yang X, Liu C, Ren P. High Order Ab Initio Valence Force Field with Chemical Pattern Based Parameter Assignment. Journal of Computational Biophysics and Chemistry. 21: 431-447. PMID 35784097 DOI: 10.1142/s2737416521420047  0.56
2021 Litman JM, Liu C, Ren P. Atomic Polarizabilities for Interactive Dipole Induction Models. Journal of Chemical Information and Modeling. PMID 34962789 DOI: 10.1021/acs.jcim.1c01307  0.528
2021 He X, Walker B, Man VH, Ren P, Wang J. Recent progress in general force fields of small molecules. Current Opinion in Structural Biology. 72: 187-193. PMID 34942567 DOI: 10.1016/j.sbi.2021.11.011  0.674
2021 Kilgour M, Liu T, Walker BD, Ren P, Simine L. E2EDNA: Simulation Protocol for DNA Aptamers with Ligands. Journal of Chemical Information and Modeling. PMID 34435773 DOI: 10.1021/acs.jcim.1c00696  0.62
2021 Walker B, Jing Z, Ren P. Molecular dynamics free energy simulations of ATP:Mg and ADP:Mg using the polarizable force field AMOEBA. Molecular Simulation. 47: 439-448. PMID 34421214 DOI: 10.1080/08927022.2020.1725003  0.734
2021 Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chemical Science. 12: 8920-8930. PMID 34257893 DOI: 10.1039/d1sc01887f  0.602
2021 El Ahdab D, Lagardère L, Inizan TJ, Célerse F, Liu C, Adjoua O, Jolly LH, Gresh N, Hobaika Z, Ren P, Maroun RG, Piquemal JP. Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface. The Journal of Physical Chemistry Letters. 6218-6226. PMID 34196568 DOI: 10.1021/acs.jpclett.1c01460  0.616
2021 Jaffrelot Inizan T, Célerse F, Adjoua O, El Ahdab D, Jolly LH, Liu C, Ren P, Montes M, Lagarde N, Lagardère L, Monmarché P, Piquemal JP. High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling. Chemical Science. 12: 4889-4907. PMID 34168762 DOI: 10.1039/d1sc00145k  0.653
2021 Jing Z, Liu C, Ren P. Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition. Journal of Chemical Information and Modeling. PMID 34096706 DOI: 10.1021/acs.jcim.1c00426  0.635
2021 Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation. PMID 33769814 DOI: 10.1021/acs.jctc.0c01286  0.824
2021 Adjoua O, Lagardère L, Jolly LH, Durocher A, Very T, Dupays I, Wang Z, Inizan TJ, Célerse F, Ren P, Ponder JW, Piquemal JP. Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems. Journal of Chemical Theory and Computation. PMID 33755446 DOI: 10.1021/acs.jctc.0c01164  0.693
2020 Adjoua O, Lagardère L, Jolly LH, Durocher A, Very T, Dupays I, Wang Z, Inizan TJ, Célerse F, Ren P, Ponder JW, Piquemal JP. Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. Arxiv. PMID 33173801  0.69
2020 El Khoury L, Célerse F, Lagardère L, Jolly LH, Derat E, Hobaika Z, Maroun RG, Ren P, Bouaziz S, Gresh N, Piquemal JP. Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations. Journal of Chemical Theory and Computation. PMID 32178519 DOI: 10.1021/Acs.Jctc.9B01204  0.427
2020 Pan C, Liu C, Peng J, Ren P, Huang X. Three-site and five-site fixed-charge water models compatible with AMOEBA force field. Journal of Computational Chemistry. PMID 31976572 DOI: 10.1002/Jcc.26151  0.599
2020 Walker B, Jing Z, Ren P. Molecular dynamics free energy simulations of ATP:Mg2+ and ADP:Mg2+ using the polarisable force field AMOEBA Molecular Simulation. 1-10. DOI: 10.1080/08927022.2020.1725003  0.722
2020 Yang X, Liu C, Walker BD, Ren P. Accurate description of molecular dipole surface with charge flux implemented for molecular mechanics Journal of Chemical Physics. 153: 64103. DOI: 10.1063/5.0016376  0.685
2019 Liu C, Piquemal JP, Ren P. Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential. The Journal of Physical Chemistry Letters. PMID 31865706 DOI: 10.1021/Acs.Jpclett.9B03489  0.654
2019 Jing Z, Qi R, Thibonnier M, Ren P. Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. Journal of Chemical Theory and Computation. PMID 31553600 DOI: 10.1021/Acs.Jctc.9B00519  0.585
2019 Chen YI, Chang YJ, Nguyen TD, Liu C, Phillion S, Kuo YA, Vu HT, Liu A, Liu YL, Hong S, Ren P, Yankeelov TE, Yeh HC. Measuring DNA hybridization kinetics in live cells using a time-resolved 3D single-molecule tracking method. Journal of the American Chemical Society. PMID 31509386 DOI: 10.1021/Jacs.9B08036  0.305
2019 Qi R, Walker B, Jing Z, Yu M, Stancu G, Edupuganti R, Dalby KN, Ren P. Computational and Experimental Studies of Inhibitor Design for Aldolase A. The Journal of Physical Chemistry. B. PMID 31268712 DOI: 10.1021/Acs.Jpcb.9B04551  0.741
2019 Liu C, Piquemal JP, Ren P. AMOEBA+ Classical Potential for Modeling Molecular Interactions. Journal of Chemical Theory and Computation. PMID 31136175 DOI: 10.1021/Acs.Jctc.9B00261  0.646
2019 Harger M, Lee JH, Walker B, Taliaferro JM, Edupuganti R, Dalby KN, Ren P. Computational insights into the binding of IN17 inhibitors to MELK. Journal of Molecular Modeling. 25: 151. PMID 31069524 DOI: 10.1007/S00894-019-4036-1  0.676
2019 Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal JP, Ren P. Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications. Annual Review of Biophysics. PMID 30916997 DOI: 10.1146/Annurev-Biophys-070317-033349  0.776
2019 Jolly L, Duran A, Lagardère L, Ponder JW, Ren P, Piquemal J. Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0] Living Journal of Computational Molecular Science. 1. DOI: 10.33011/Livecoms.1.2.10409  0.672
2018 Meng F, Jing Z, Ferreira R, Ren P, Zhang F. Investigating the Association Mechanism between Rafoxanide and Povidone. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 30360618 DOI: 10.1021/Acs.Langmuir.8B03174  0.512
2018 Rackers JA, Liu C, Ren P, Ponder JW. A physically grounded damped dispersion model with particle mesh Ewald summation. The Journal of Chemical Physics. 149: 084115. PMID 30193468 DOI: 10.1063/1.5030434  0.718
2018 Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. Journal of Chemical Theory and Computation. 14: 5273-5289. PMID 30176213 DOI: 10.1021/Acs.Jctc.8B00529  0.801
2018 Jing Z, Liu C, Qi R, Ren P. Many-body effect determines the selectivity for Ca and Mg in proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 30038003 DOI: 10.1073/Pnas.1805049115  0.643
2018 Qi R, Jing Z, Liu C, Piquemal JP, Dalby KN, Ren P. Elucidating the Phosphate Binding Mode of PBP: The Critical Effect of Buffer Solution. The Journal of Physical Chemistry. B. PMID 29807433 DOI: 10.1021/Acs.Jpcb.8B03194  0.664
2018 Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chemical Science. 9: 956-972. PMID 29732110 DOI: 10.1039/C7Sc04531J  0.82
2018 Zhang C, Lu C, Jing Z, Wu C, Piquemal JP, Ponder JW, Ren P. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. Journal of Chemical Theory and Computation. PMID 29438622 DOI: 10.1021/Acs.Jctc.7B01169  0.742
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  0.443
2017 Jing Z, Qi R, Liu C, Ren P. Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field. The Journal of Chemical Physics. 147: 161733. PMID 29096462 DOI: 10.1063/1.4985921  0.682
2017 Han X, Jing Z, Wu W, Zou B, Peng Z, Ren P, Wikramanayake A, Lu Z, Leblanc RM. Biocompatible and blood-brain barrier permeable carbon dots for inhibition of Aβ fibrillation and toxicity, and BACE1 activity. Nanoscale. PMID 28850143 DOI: 10.1039/C7Nr04352J  0.389
2017 Deng S, Wang Q, Ren P. Estimating and modeling charge transfer from the SAPT induction energy. Journal of Computational Chemistry. PMID 28766729 DOI: 10.1002/Jcc.24864  0.437
2017 Harger M, Li D, Wang Z, Dalby K, Lagardère L, Piquemal JP, Ponder J, Ren P. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. Journal of Computational Chemistry. 38: 2047-2055. PMID 28600826 DOI: 10.1002/Jcc.24853  0.687
2017 Liu C, Qi R, Wang Q, Piquemal JP, Ren P. Capturing Many-body Interactions with Classical Dipole Induction Models. Journal of Chemical Theory and Computation. PMID 28482664 DOI: 10.1021/Acs.Jctc.7B00225  0.598
2017 Bell DR, Cheng SY, Salazar H, Ren P. Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations. Scientific Reports. 7: 45812. PMID 28393861 DOI: 10.1038/Srep45812  0.408
2017 Aviat F, Levitt A, Stamm B, Maday Y, Ren P, Ponder JW, Lagardère L, Piquemal JP. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations. Journal of Chemical Theory and Computation. 13: 180-190. PMID 28068773 DOI: 10.1021/Acs.Jctc.6B00981  0.667
2016 Zhang C, Bell D, Harger M, Ren P. Polarizable Multipole-based Force Field for Aromatic Molecules and Nucleobases. Journal of Chemical Theory and Computation. PMID 28030769 DOI: 10.1021/Acs.Jctc.6B00918  0.496
2016 Rackers JA, Wang Q, Liu C, Piquemal JP, Ren P, Ponder JW. An optimized charge penetration model for use with the AMOEBA force field. Physical Chemistry Chemical Physics : Pccp. PMID 27901142 DOI: 10.1039/C6Cp06017J  0.756
2016 Qi R, Wang Q, Ren P. General van der Waals potential for common organic molecules. Bioorganic & Medicinal Chemistry. PMID 27519463 DOI: 10.1016/J.Bmc.2016.07.062  0.387
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  0.416
2016 Bell DR, Qi R, Jing Z, Xiang JY, Mejias C, Schnieders MJ, Ponder JW, Ren P. Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field. Physical Chemistry Chemical Physics : Pccp. PMID 27254477 DOI: 10.1039/C6Cp02509A  0.814
2016 Narth C, Lagardère L, Polack É, Gresh N, Wang Q, Bell DR, Rackers JA, Ponder JW, Ren PY, Piquemal JP. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. Journal of Computational Chemistry. 37: 494-506. PMID 26814845 DOI: 10.1002/Jcc.24257  0.685
2016 Gao Y, Hu Y, Ren P, Zhou D, Qiu J. Effect of Li+ ions on the enhancement upconversion and stokes emission of NaYF4:Tb, Yb co-doped in glass-ceramics Journal of Alloys and Compounds. 667: 297-301. DOI: 10.1016/j.jallcom.2016.01.200  0.34
2015 Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald. Journal of Chemical Theory and Computation. 11: 2589-99. PMID 26575557 DOI: 10.1021/Acs.Jctc.5B00171  0.75
2015 Zhang C, Lu C, Wang Q, Ponder JW, Ren P. Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate. Journal of Chemical Theory and Computation. 11: 5326-39. PMID 26574325 DOI: 10.1021/Acs.Jctc.5B00562  0.744
2015 Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP. Polarizable molecular dynamics in a polarizable continuum solvent. Journal of Chemical Theory and Computation. 11: 623-34. PMID 26516318 DOI: 10.1021/Ct500998Q  0.748
2015 Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field. Journal of Chemical Theory and Computation. 11: 2609-2618. PMID 26413036 DOI: 10.1021/Acs.Jctc.5B00267  0.738
2015 Qi R, Wang LP, Wang Q, Pande VS, Ren P. United polarizable multipole water model for molecular mechanics simulation. The Journal of Chemical Physics. 143: 014504. PMID 26156485 DOI: 10.1063/1.4923338  0.464
2015 Wang Q, Edupuganti R, Tavares CD, Dalby KN, Ren P. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis. Frontiers in Molecular Biosciences. 2: 9. PMID 25988177 DOI: 10.3389/Fmolb.2015.00009  0.413
2015 Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field Journal of Chemical Theory and Computation. 11: 2609-2618. DOI: 10.1021/acs.jctc.5b00267  0.686
2015 Torabifard H, Starovoytov ON, Ren P, Cisneros GA. Development of an AMOEBA water model using GEM distributed multipoles Theoretical Chemistry Accounts. 134. DOI: 10.1007/S00214-015-1702-Y  0.414
2014 Lagardère L, Lipparini F, Polack É, Stamm B, Cancès É, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald. Journal of Chemical Theory and Computation. 10: 1638-1651. PMID 26512230 DOI: 10.1021/Ct401096T  0.75
2014 Marjolin A, Gourlaouen C, Clavaguéra C, Ren PY, Piquemal JP, Dognon JP. Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics. Journal of Molecular Modeling. 20: 2471. PMID 25296890 DOI: 10.1007/S00894-014-2471-6  0.401
2014 Abella JR, Cheng SY, Wang Q, Yang W, Ren P. Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field. Journal of Chemical Theory and Computation. 10: 2792-2801. PMID 25018674 DOI: 10.1021/Ct500202Q  0.486
2014 Shen H, Li Y, Ren P, Zhang D, Li G. An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials. Journal of Chemical Theory and Computation. 10: 731-750. PMID 24659927 DOI: 10.1021/Ct400974Z  0.436
2014 Mu X, Wang Q, Wang LP, Fried SD, Piquemal JP, Dalby KN, Ren P. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. The Journal of Physical Chemistry. B. 118: 6456-65. PMID 24484473 DOI: 10.1021/Jp411671A  0.453
2014 Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chemical Reviews. 114: 779-814. PMID 23981057 DOI: 10.1021/Cr300461D  0.359
2014 Cisneros GA, Karttunen M, Ren P, Sagui C. Correction to Classical Electrostatics for Biomolecular Simulations Chemical Reviews. 114: 5116-5116. DOI: 10.1021/Cr500124K  0.478
2014 Wang L, Head-Gordon T, Ponder J, Ren P, Chodera J, Eastman P, Martinez TJ, Pande VS. Systematic Improvement on the Classical Molecular Model of Water Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2273  0.666
2013 Fried SD, Wang LP, Boxer SG, Ren P, Pande VS. Calculations of the electric fields in liquid solutions. The Journal of Physical Chemistry. B. 117: 16236-48. PMID 24304155 DOI: 10.1021/Jp410720Y  0.483
2013 Shi Y, Xia Z, Zhang J, Best R, Wu C, Ponder JW, Ren P. The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation. 9: 4046-4063. PMID 24163642 DOI: 10.1021/Ct4003702  0.745
2013 Dykstra DW, Dalby KN, Ren P. Elucidating binding modes of zuonin A enantiomers to JNK1 via in silico methods. Journal of Molecular Graphics & Modelling. 45: 38-44. PMID 24001752 DOI: 10.1016/J.Jmgm.2013.08.008  0.365
2013 Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS. Systematic improvement of a classical molecular model of water. The Journal of Physical Chemistry. B. 117: 9956-72. PMID 23750713 DOI: 10.1021/Jp403802C  0.671
2013 Xia Z, Bell DR, Shi Y, Ren P. RNA 3D structure prediction by using a coarse-grained model and experimental data. The Journal of Physical Chemistry. B. 117: 3135-44. PMID 23438338 DOI: 10.1021/Jp400751W  0.309
2013 Wu X, Shi Y, Ren P, Wang D, Li G. Exploring the relationship between sequences, structures, dynamical behaviors and functions of new type protein drugs: DARPins. Current Pharmaceutical Design. 19: 2308-17. PMID 23082980 DOI: 10.2174/1381612811319120017  0.36
2013 Fu T, Ren H, Zhang J, Ren P, Enyedy I, Li G. Role of bivalent cations in structural stabilities of new drug targets--vaccinia-related kinases (VRK) from molecular dynamics simulations. Current Pharmaceutical Design. 19: 2269-81. PMID 23082977 DOI: 10.2174/1381612811319120014  0.401
2012 Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Quarterly Reviews of Biophysics. 45: 427-91. PMID 23217364 DOI: 10.1017/S003358351200011X  0.737
2012 Mu X, Eckes KM, Nguyen MM, Suggs LJ, Ren P. Experimental and computational studies reveal an alternative supramolecular structure for fmoc-dipeptide self-assembly. Biomacromolecules. 13: 3562-71. PMID 23020140 DOI: 10.1021/Bm301007R  0.341
2012 Kaoud TS, Park H, Mitra S, Yan C, Tseng CC, Shi Y, Jose J, Taliaferro JM, Lee K, Ren P, Hong J, Dalby KN. Manipulating JNK signaling with (--)-zuonin A. Acs Chemical Biology. 7: 1873-83. PMID 22916726 DOI: 10.1021/Cb300261E  0.306
2012 Zhang J, Yang W, Piquemal JP, Ren P. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. Journal of Chemical Theory and Computation. 8: 1314-1324. PMID 22754403 DOI: 10.1021/Ct200812Y  0.398
2012 Xiong R, Cai XM, Wei J, Ren PY. Some insights into the binding mechanism of Aurora B kinase gained by molecular dynamics simulation. Journal of Molecular Modeling. 18: 4591-601. PMID 22643974 DOI: 10.1007/S00894-012-1453-9  0.392
2012 Schnieders MJ, Baltrusaitis J, Shi Y, Chattree G, Zheng L, Yang W, Ren P. The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field. Journal of Chemical Theory and Computation. 8: 1721-1736. PMID 22582032 DOI: 10.1021/Ct300035U  0.748
2012 Wu JC, Chattree G, Ren P. Automation of AMOEBA polarizable force field parameterization for small molecules. Theoretical Chemistry Accounts. 131: 1138. PMID 22505837 DOI: 10.1007/S00214-012-1138-6  0.491
2012 Schnieders MJ, Kaoud TS, Yan C, Dalby KN, Ren P. Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases. Current Pharmaceutical Design. 18: 1173-85. PMID 22316156 DOI: 10.2174/138920012799362873  0.669
2012 Shi Y, Zhu CZ, Martin SF, Ren P. Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations. The Journal of Physical Chemistry. B. 116: 1716-27. PMID 22214214 DOI: 10.1021/Jp210265D  0.419
2012 Xia Z, Clark P, Huynh T, Loher P, Zhao Y, Chen HW, Ren P, Rigoutsos I, Zhou R. ERRATUM: Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets (Scientific Reports (2012) 2 (569) DOI: 10.1038/srep00569) Scientific Reports. 2: 909. DOI: 10.1038/Srep00909  0.337
2012 Schnieders MJ, Shi Y, Wu J, Baltrusaitis J, Yang W, Ren P. Pharmaceutical Applications of the Polarizable Amoeba Potential, Including Protein-Ligand Binding Affinity and Drug Solubility, using the Force Field X Software Biophysical Journal. 102: 409a-410a. DOI: 10.1016/J.Bpj.2011.11.2239  0.761
2012 Shen H, Xia Z, Li G, Ren P. A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics Annual Reports in Computational Chemistry. 8: 129-148. DOI: 10.1016/B978-0-444-59440-2.00005-3  0.463
2012 Marjolin A, Gourlaouen C, Clavaguéra C, Ren PY, Wu JC, Gresh N, Dognon JP, Piquemal JP. Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: From gas-phase energetics to hydration free energies Theoretical Chemistry Accounts. 131: 1-14. DOI: 10.1007/S00214-012-1198-7  0.418
2011 Kryscio DR, Shi Y, Ren P, Peppas NA. Molecular docking simulations for macromolecularly imprinted polymers. Industrial & Engineering Chemistry Research. 50: 13877-13884. PMID 22287827 DOI: 10.1021/Ie201858N  0.394
2011 Wu J, Zhen X, Shen H, Li G, Ren P. Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent. The Journal of Chemical Physics. 135: 155104. PMID 22029338 DOI: 10.1063/1.3651626  0.487
2011 Ren P, Wu C, Ponder JW. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. Journal of Chemical Theory and Computation. 7: 3143-3161. PMID 22022236 DOI: 10.1021/Ct200304D  0.721
2011 Gardner DP, Ren P, Ozer S, Gutell RR. Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure. Journal of Molecular Biology. 413: 473-83. PMID 21889515 DOI: 10.1016/J.Jmb.2011.08.033  0.317
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  0.453
2011 Piserchio A, Warthaka M, Devkota AK, Kaoud TS, Lee S, Abramczyk O, Ren P, Dalby KN, Ghose R. Solution NMR insights into docking interactions involving inactive ERK2. Biochemistry. 50: 3660-72. PMID 21449613 DOI: 10.1021/Bi2000559  0.32
2011 Yan C, Kaoud T, Lee S, Dalby KN, Ren P. Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1. The Journal of Physical Chemistry. B. 115: 1491-502. PMID 21261310 DOI: 10.1021/Jp1073522  0.378
2011 Shi Y, Wu C, Ponder JW, Ren P. Multipole electrostatics in hydration free energy calculations. Journal of Computational Chemistry. 32: 967-77. PMID 20925089 DOI: 10.1002/Jcc.21681  0.711
2010 Wu JC, Piquemal JP, Chaudret R, Reinhardt P, Ren P. Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. Journal of Chemical Theory and Computation. 6: 2059-2070. PMID 21116445 DOI: 10.1021/Ct100091J  0.465
2010 Fonner JM, Schmidt CE, Ren P. A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole. Polymer. 51: 4985-4993. PMID 21052521 DOI: 10.1016/J.Polymer.2010.08.024  0.476
2010 Xia Z, Gardner DP, Gutell RR, Ren P. Coarse-grained model for simulation of RNA three-dimensional structures. The Journal of Physical Chemistry. B. 114: 13497-506. PMID 20883011 DOI: 10.1021/Jp104926T  0.371
2010 Yan C, Pattani V, Tunnell JW, Ren P. Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation. Journal of Molecular Graphics & Modelling. 29: 2-12. PMID 20466569 DOI: 10.1016/J.Jmgm.2010.03.011  0.379
2010 Zhang J, King CA, Dalby K, Ren P. Conformational preference of ChaK1 binding peptides: a molecular dynamics study. Pmc Biophysics. 3: 2. PMID 20180991 DOI: 10.1186/1757-5036-3-2  0.327
2010 Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/Jp910674D  0.835
2009 Shi Y, Jiao D, Schnieders MJ, Ren P. Trypsin-ligand binding free energy calculation with AMOEBA. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 2328-31. PMID 19965178 DOI: 10.1109/IEMBS.2009.5335108  0.765
2009 Wu JC, Gardner DP, Ozer S, Gutell RR, Ren P. Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding. Journal of Molecular Biology. 391: 769-83. PMID 19540243 DOI: 10.1016/J.Jmb.2009.06.036  0.341
2009 Jiao D, Zhang J, Duke RE, Li G, Schnieders MJ, Ren P. Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. Journal of Computational Chemistry. 30: 1701-11. PMID 19399779 DOI: 10.1002/Jcc.21268  0.778
2008 Golubkov PA, Wu JC, Ren P. A transferable coarse-grained model for hydrogen-bonding liquids. Physical Chemistry Chemical Physics : Pccp. 10: 2050-7. PMID 18688358 DOI: 10.1039/B715841F  0.436
2008 Jiao D, Golubkov PA, Darden TA, Ren P. Calculation of protein-ligand binding free energy by using a polarizable potential. Proceedings of the National Academy of Sciences of the United States of America. 105: 6290-5. PMID 18427113 DOI: 10.1073/Pnas.0711686105  0.642
2007 Zhang J, King M, Suggs L, Ren P. Molecular modeling of conformational properties of oligodepsipeptides. Biomacromolecules. 8: 3015-24. PMID 17877396 DOI: 10.1021/Bm070244C  0.379
2007 Schnieders MJ, Baker NA, Ren P, Ponder JW. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. The Journal of Chemical Physics. 126: 124114. PMID 17411115 DOI: 10.1063/1.2714528  0.822
2007 Rasmussen TD, Ren P, Ponder JW, Jensen F. Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization International Journal of Quantum Chemistry. 107: 1390-1395. DOI: 10.1002/Qua.21278  0.716
2006 Jiao D, King C, Grossfield A, Darden TA, Ren P. Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. The Journal of Physical Chemistry. B. 110: 18553-9. PMID 16970483 DOI: 10.1021/Jp062230R  0.591
2006 Golubkov PA, Ren P. Generalized coarse-grained model based on point multipole and Gay-Berne potentials. The Journal of Chemical Physics. 125: 64103. PMID 16942269 DOI: 10.1063/1.2244553  0.444
2006 Piquemal JP, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. The Journal of Chemical Physics. 125: 054511. PMID 16942230 DOI: 10.1063/1.2234774  0.505
2004 Ren P, Ponder JW. Temperature and pressure dependence of the AMOEBA water model Journal of Physical Chemistry B. 108: 13427-13437. DOI: 10.1021/Jp0484332  0.648
2003 Grossfield A, Ren P, Ponder JW. Ion solvation thermodynamics from simulation with a polarizable force field. Journal of the American Chemical Society. 125: 15671-82. PMID 14664617 DOI: 10.1021/Ja037005R  0.723
2003 Ren P, Ponder JW. Polarizable atomic multipole water model for molecular mechanics simulation Journal of Physical Chemistry B. 107: 5933-5947. DOI: 10.1021/Jp027815+  0.691
2002 Ren P, Ponder JW. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. Journal of Computational Chemistry. 23: 1497-506. PMID 12395419 DOI: 10.1002/Jcc.10127  0.672
2000 Fried JR, Ren P. The atomistic simulation of the gas permeability of poly(organophosphazenes). Part 1. Poly(dibutoxyphosphazenes) Computational and Theoretical Polymer Science. 10: 447-463. DOI: 10.1016/S1089-3156(00)00005-2  0.706
1999 Fried JR, Ren P. Molecular simulation of the glass transition of polyphosphazenes Computational and Theoretical Polymer Science. 9: 111-116. DOI: 10.1016/S1089-3156(99)00002-1  0.722
1998 Sun H, Ren P, Fried J. The COMPASS force field: parameterization and validation for phosphazenes Computational and Theoretical Polymer Science. 8: 229-246. DOI: 10.1016/S1089-3156(98)00042-7  0.819
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