Pengyu Ren - Publications

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

111 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
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  0.64
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  0.64
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  0.56
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  0.64
2019 Lee EY, Zhang C, Di Domizio J, Jin F, Connell W, Hung M, Malkoff N, Veksler V, Gilliet M, Ren P, Wong GCL. Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsDNA to TLR9. Nature Communications. 10: 1012. PMID 30833557 DOI: 10.1038/s41467-019-08868-w  0.52
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  0.64
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  0.64
2018 Rackers JA, Wang Z, Lu C, Laury ML, Lagardere L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. Journal of Chemical Theory and Computation. PMID 30176213 DOI: 10.1021/acs.jctc.8b00529  0.56
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  0.64
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  0.64
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  0.56
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  0.64
2018 Zhao J, Wang G, Del Mundo IM, McKinney JA, Lu X, Bacolla A, Boulware SB, Zhang C, Zhang H, Ren P, Freudenreich CH, Vasquez KM. Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes. Cell Reports. 22: 1200-1210. PMID 29386108 DOI: 10.1016/j.celrep.2018.01.014  0.52
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  0.64
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  0.64
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  0.56
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  0.64
2017 Obliosca JM, Cheng SY, Chen YA, Llanos MF, Liu YL, Imphean DM, Bell D, Petty JT, Ren P, Yeh HC. LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature. Journal of the American Chemical Society. PMID 28463488 DOI: 10.1021/jacs.7b03395  0.36
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  0.36
2017 Edupuganti R, Taliaferro JM, Wang Q, Xie X, Cho EJ, Vidhu F, Ren P, Anslyn EV, Bartholomeusz C, Dalby KN. Discovery of a potent inhibitor of MELK that inhibits expression of the anti-apoptotic protein Mcl-1 and TNBC cell growth. Bioorganic & Medicinal Chemistry. PMID 28351607 DOI: 10.1016/j.bmc.2017.03.018  0.56
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  0.56
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  0.52
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  0.64
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  0.64
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  0.64
2016 Liu X, Tan Y, Zhang C, Zhang Y, Zhang L, Ren P, Deng H, Luo J, Ke Y, Du X. NAT10 regulates p53 activation through acetylating p53 at K120 and ubiquitinating Mdm2. Embo Reports. PMID 26882543 DOI: 10.15252/embr.201540505  0.52
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  0.56
2016 Houser JR, Busch DJ, Bell DR, Li B, Ren P, Stachowiak JC. The impact of physiological crowding on the diffusivity of membrane bound proteins. Soft Matter. PMID 26751985 DOI: 10.1039/c5sm02572a  0.52
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  0.56
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  0.52
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  0.56
2015 Yu J, Ren P, Zhong T, Wang Y, Yan M, Xue B, Li R, Dai C, Liu C, Chen G, Yu XF. Pseudolaric acid B inhibits proliferation in SW579 human thyroid squamous cell carcinoma. Molecular Medicine Reports. PMID 26460192 DOI: 10.3892/mmr.2015.4418  0.64
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  0.64
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  0.52
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  0.56
2015 Warthaka M, Adelmann CH, Kaoud TS, Edupuganti R, Yan C, Johnson WH, Ferguson S, Tavares CD, Pence LJ, Anslyn EV, Ren P, Tsai KY, Dalby KN. Quantification of a Pharmacodynamic ERK End Point in Melanoma Cell Lysates: Toward Personalized Precision Medicine. Acs Medicinal Chemistry Letters. 6: 47-52. PMID 25589929 DOI: 10.1021/ml500198b  0.52
2015 Li J, Ma Y, Ren P, Zhang C. 10×200 Gb/s real-time transmission over 2000km with commercial devices, flex-grid, flexible modulation format and 5 types of fiber 2015 Opto-Electronics and Communications Conference, Oecc 2015. DOI: 10.1109/OECC.2015.7340062  0.52
2015 Wang R, Ren P, Liu C, Guo S, Huang R. Understanding NBTI-induced dynamic variability in the nano-reliability Era: From devices to circuits Proceedings of the International Symposium On the Physical and Failure Analysis of Integrated Circuits, Ipfa. 2015: 119-121. DOI: 10.1109/IPFA.2015.7224347  0.64
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: 623-634. DOI: 10.1021/ct500998q  0.52
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  0.52
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: 2589-2599. DOI: 10.1021/acs.jctc.5b00171  0.52
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  0.52
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  0.56
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  0.52
2014 Devkota AK, Edupuganti R, Yan C, Shi Y, Jose J, Wang Q, Kaoud TS, Cho EJ, Ren P, Dalby KN. Reversible covalent inhibition of eEF-2K by carbonitriles. Chembiochem : a European Journal of Chemical Biology. 15: 2435-42. PMID 25224652 DOI: 10.1002/cbic.201402321  0.52
2014 Edupuganti R, Wang Q, Tavares CD, Chitjian CA, Bachman JL, Ren P, Anslyn EV, Dalby KN. Synthesis and biological evaluation of pyrido[2,3-d]pyrimidine-2,4-dione derivatives as eEF-2K inhibitors. Bioorganic & Medicinal Chemistry. 22: 4910-6. PMID 25047940 DOI: 10.1016/j.bmc.2014.06.050  0.52
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  0.52
2014 Tavares CD, Ferguson SB, Giles DH, Wang Q, Wellmann RM, O'Brien JP, Warthaka M, Brodbelt JS, Ren P, Dalby KN. The molecular mechanism of eukaryotic elongation factor 2 kinase activation. The Journal of Biological Chemistry. 289: 23901-16. PMID 25012662 DOI: 10.1074/jbc.M114.577148  0.52
2014 Eckes KM, Mu X, Ruehle MA, Ren P, Suggs LJ. β sheets not required: combined experimental and computational studies of self-assembly and gelation of the ester-containing analogue of an Fmoc-dipeptide hydrogelator. Langmuir : the Acs Journal of Surfaces and Colloids. 30: 5287-96. PMID 24786493 DOI: 10.1021/la500679b  0.52
2014 Wang Q, Park J, Devkota AK, Cho EJ, Dalby KN, Ren P. Identification and validation of novel PERK inhibitors. Journal of Chemical Information and Modeling. 54: 1467-75. PMID 24745945 DOI: 10.1021/ci500114r  0.52
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  0.52
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  0.52
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  0.52
2014 Lipparini F, Lagardère L, Stamm B, Cancès E, Schnieders M, Ren P, Maday Y, Piquemal JP. Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: I. Toward massively parallel direct space computations Journal of Chemical Theory and Computation. 10: 1638-1651. DOI: 10.1021/ct401096t  0.52
2013 Liu C, Xu HH, Zou QY, Guo X, Liu ZZ, Luo ZQ, Li Y, Qi J, Liu J, Ren PY, Fan YY. [Treatment of unstable lumbar intervertebral disc herniation by modified lamina osteotomy replantation]. Zhongguo Gu Shang = China Journal of Orthopaedics and Traumatology. 26: 918-22. PMID 24605743  0.64
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
2013 Xia Z, Huynh T, Ren P, Zhou R. Large domain motions in Ago protein controlled by the guide DNA-strand seed region determine the Ago-DNA-mRNA complex recognition process. Plos One. 8: e54620. PMID 23382927 DOI: 10.1371/journal.pone.0054620  0.52
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  0.52
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  0.52
2013 Bell DR, Xia Z, Ren P. Multiscale modeling of RNA 3D structures Proceedings of the 2013 4th Annual Ornl Biomedical Sciences and Engineering Conference: Collaborative Biomedical Innovations, Bsec 2013. DOI: 10.1109/BSEC.2013.6618482  0.52
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  0.52
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  0.52
2012 Kaoud TS, Yan C, Mitra S, Tseng CC, Jose J, Taliaferro JM, Tuohetahuntila M, Devkota A, Sammons R, Park J, Park H, Shi Y, Hong J, Ren P, Dalby KN. From in Silico Discovery to intra-Cellular Activity: Targeting JNK-Protein Interactions with Small Molecules. Acs Medicinal Chemistry Letters. 3: 721-725. PMID 23002419 DOI: 10.1021/ml300129b  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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: 10.2174/138161212799436368  0.52
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  0.52
2012 Chaudret R, De Courcy B, Marjolin A, Van Severen MC, Ren PY, Wu JC, Parisel O, Piquemal JP. Unraveling interactions in large complex systems using quantum chemistry interpretative techniques and new generation polarizable force fields Aip Conference Proceedings. 1504: 699-702. DOI: 10.1063/1.4771791  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
2011 Lee S, Warthaka M, Yan C, Kaoud TS, Ren P, Dalby KN. Examining docking interactions on ERK2 with modular peptide substrates. Biochemistry. 50: 9500-10. PMID 21955038 DOI: 10.1021/bi201103b  0.52
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  0.52
2011 Lee S, Warthaka M, Yan C, Kaoud TS, Piserchio A, Ghose R, Ren P, Dalby KN. A model of a MAPK•substrate complex in an active conformation: a computational and experimental approach. Plos One. 6: e18594. PMID 21494553 DOI: 10.1371/journal.pone.0018594  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
2010 Callaway K, Waas WF, Rainey MA, Ren P, Dalby KN. Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1. Biochemistry. 49: 3619-30. PMID 20361728 DOI: 10.1021/bi100199q  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
2008 Li HX, Hwang BY, Laxmikanthan G, Blaber SI, Blaber M, Golubkov PA, Ren P, Iverson BL, Georgiou G. Substrate specificity of human kallikreins 1 and 6 determined by phage display. Protein Science : a Publication of the Protein Society. 17: 664-72. PMID 18359858 DOI: 10.1110/ps.073333208  0.32
2008 Nguyen M, Suggs L, Ren P. Synthesis of polydepsipeptides for tissue engineering 8th World Biomaterials Congress 2008. 3: 1650.  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
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  0.52
2003 Ren P, Ponder JW. Polarizable atomic multipole water model for molecular mechanics simulation Journal of Physical Chemistry B. 107: 5933-5947.  0.52
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  0.52
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