Publications

Link to Google Scholar

  • [DOI] E. Y. Lee, C. Zhang, J. Di Domizio, F. Jin, W. Connell, M. Hung, N. Malkoff, V. Veksler, M. Gilliet, P. Ren, and G. C. L. Wong, “Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsdna to tlr9,” Nature communications, vol. 10, iss. 1, p. 1012, 2019.
    [Bibtex]
    @article{RN144,
    author = {Lee, Ernest Y. and Zhang, Changsheng and Di Domizio, Jeremy and Jin, Fan and Connell, Will and Hung, Mandy and Malkoff, Nicolas and Veksler, Veronica and Gilliet, Michel and Ren, Pengyu and Wong, Gerard C. L.},
    title = {Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsDNA to TLR9},
    journal = {Nature Communications},
    volume = {10},
    number = {1},
    pages = {1012},
    ISSN = {2041-1723},
    DOI = {10.1038/s41467-019-08868-w},
    url = {https://doi.org/10.1038/s41467-019-08868-w},
    year = {2019},
    type = {Journal Article}
    }
  • [DOI] J. Zhao, G. Wang, I. M. Del Mundo, J. A. McKinney, X. Lu, A. Bacolla, S. B. Boulware, C. Zhang, H. Zhang, P. Ren, C. H. Freudenreich, and K. M. Vasquez, “Distinct mechanisms of nuclease-directed dna-structure-induced genetic instability in cancer genomes,” Cell rep, vol. 22, iss. 5, pp. 1200-1210, 2018.
    [Bibtex]
    @article{RN139,
    author = {Zhao, J. and Wang, G. and Del Mundo, I. M. and McKinney, J. A. and Lu, X. and Bacolla, A. and Boulware, S. B. and Zhang, C. and Zhang, H. and Ren, P. and Freudenreich, C. H. and Vasquez, K. M.},
    title = {Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes},
    journal = {Cell Rep},
    volume = {22},
    number = {5},
    pages = {1200-1210},
    ISSN = {2211-1247 (Electronic)},
    DOI = {10.1016/j.celrep.2018.01.014},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/29386108},
    year = {2018},
    type = {Journal Article}
    }
  • [DOI] J. A. Rackers, C. Liu, P. Ren, and J. W. Ponder, “A physically grounded damped dispersion model with particle mesh ewald summation,” J chem phys, vol. 149, iss. 8, p. 84115, 2018.
    [Bibtex]
    @article{RN142,
    author = {Rackers, J. A. and Liu, C. and Ren, P. and Ponder, J. W.},
    title = {A physically grounded damped dispersion model with particle mesh Ewald summation},
    journal = {J Chem Phys},
    volume = {149},
    number = {8},
    pages = {084115},
    ISSN = {1089-7690 (Electronic)
    0021-9606 (Linking)},
    DOI = {10.1063/1.5030434},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/30193468},
    year = {2018},
    type = {Journal Article}
    }
  • [DOI] Z. Jing, C. Liu, R. Qi, and P. Ren, “Many-body effect determines the selectivity for ca(2+) and mg(2+) in proteins,” Proc natl acad sci u s a, vol. 115, iss. 32, p. E7495-E7501, 2018.
    [Bibtex]
    @article{RN141,
    author = {Jing, Z. and Liu, C. and Qi, R. and Ren, P.},
    title = {Many-body effect determines the selectivity for Ca(2+) and Mg(2+) in proteins},
    journal = {Proc Natl Acad Sci U S A},
    volume = {115},
    number = {32},
    pages = {E7495-E7501},
    ISSN = {1091-6490 (Electronic)
    0027-8424 (Linking)},
    DOI = {10.1073/pnas.1805049115},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/30038003},
    year = {2018},
    type = {Journal Article}
    }
  • [DOI] C. Zhang, C. Lu, Z. Jing, C. Wu, J. P. Piquemal, J. W. Ponder, and P. Ren, “Amoeba polarizable atomic multipole force field for nucleic acids,” J chem theory comput, vol. 14, iss. 4, pp. 2084-2108, 2018.
    [Bibtex]
    @article{RN138,
    author = {Zhang, C. and Lu, C. and Jing, Z. and Wu, C. and Piquemal, J. P. and Ponder, J. W. and Ren, P.},
    title = {AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids},
    journal = {J Chem Theory Comput},
    volume = {14},
    number = {4},
    pages = {2084-2108},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/acs.jctc.7b01169},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/29438622},
    year = {2018},
    type = {Journal Article}
    }
  • [DOI] L. Lagardere, L. H. Jolly, F. Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders, N. Gresh, Y. Maday, P. Y. Ren, J. W. Ponder, and J. P. Piquemal, “Tinker-hp: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields,” Chem sci, vol. 9, iss. 4, pp. 956-972, 2018.
    [Bibtex]
    @article{RN136,
    author = {Lagardere, L. and Jolly, L. H. and Lipparini, F. and Aviat, F. and Stamm, B. and Jing, Z. F. and Harger, M. and Torabifard, H. and Cisneros, G. A. and Schnieders, M. J. and Gresh, N. and Maday, Y. and Ren, P. Y. and Ponder, J. W. and Piquemal, J. P.},
    title = {Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields},
    journal = {Chem Sci},
    volume = {9},
    number = {4},
    pages = {956-972},
    ISSN = {2041-6520 (Print)
    2041-6520 (Linking)},
    DOI = {10.1039/c7sc04531j},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/29732110},
    year = {2018},
    type = {Journal Article}
    }
  • [DOI] J. A. Rackers, Z. Wang, C. Lu, M. L. Laury, L. Lagardere, M. J. Schnieders, J. P. Piquemal, P. Ren, and J. W. Ponder, “Tinker 8: software tools for molecular design,” J chem theory comput, vol. 14, iss. 10, pp. 5273-5289, 2018.
    [Bibtex]
    @article{RN143,
    author = {Rackers, J. A. and Wang, Z. and Lu, C. and Laury, M. L. and Lagardere, L. and Schnieders, M. J. and Piquemal, J. P. and Ren, P. and Ponder, J. W.},
    title = {Tinker 8: Software Tools for Molecular Design},
    journal = {J Chem Theory Comput},
    volume = {14},
    number = {10},
    pages = {5273-5289},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/acs.jctc.8b00529},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/30176213},
    year = {2018},
    type = {Journal Article}
    }
  • [DOI] R. Qi, Z. Jing, C. Liu, J. P. Piquemal, K. N. Dalby, and P. Ren, “Elucidating the phosphate binding mode of phosphate-binding protein: the critical effect of buffer solution,” J phys chem b, vol. 122, iss. 24, pp. 6371-6376, 2018.
    [Bibtex]
    @article{RN130,
    author = {Qi, R. and Jing, Z. and Liu, C. and Piquemal, J. P. and Dalby, K. N. and Ren, P.},
    title = {Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution},
    journal = {J Phys Chem B},
    volume = {122},
    number = {24},
    pages = {6371-6376},
    ISSN = {1520-5207 (Electronic)
    1520-5207 (Linking)},
    DOI = {10.1021/acs.jpcb.8b03194},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/29807433},
    year = {2018},
    type = {Journal Article}
    }
  • [DOI] Z. Jing, R. Qi, C. Liu, and P. Ren, “Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the amoeba force field,” J chem phys, vol. 147, iss. 16, p. 161733, 2017.
    [Bibtex]
    @article{RN140,
    author = {Jing, Z. and Qi, R. and Liu, C. and Ren, P.},
    title = {Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field},
    journal = {J Chem Phys},
    volume = {147},
    number = {16},
    pages = {161733},
    ISSN = {1089-7690 (Electronic)
    0021-9606 (Linking)},
    DOI = {10.1063/1.4985921},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/29096462},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] C. Liu, R. Qi, Q. Wang, J. P. Piquemal, and P. Ren, “Capturing many-body interactions with classical dipole induction models,” J chem theory comput, vol. 13, iss. 6, pp. 2751-2761, 2017.
    [Bibtex]
    @article{RN110,
    author = {Liu, C. and Qi, R. and Wang, Q. and Piquemal, J. P. and Ren, P.},
    title = {Capturing Many-Body Interactions with Classical Dipole Induction Models},
    journal = {J Chem Theory Comput},
    volume = {13},
    number = {6},
    pages = {2751-2761},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/acs.jctc.7b00225},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28482664},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] J. M. Obliosca, S. Y. Cheng, Y. A. Chen, M. F. Llanos, Y. L. Liu, D. M. Imphean, D. R. Bell, J. T. Petty, P. Ren, and H. C. Yeh, “Lna thymidine monomer enables differentiation of the four single-nucleotide variants by melting temperature,” J am chem soc, vol. 139, iss. 20, pp. 7110-7116, 2017.
    [Bibtex]
    @article{RN109,
    author = {Obliosca, J. M. and Cheng, S. Y. and Chen, Y. A. and Llanos, M. F. and Liu, Y. L. and Imphean, D. M. and Bell, D. R. and Petty, J. T. and Ren, P. and Yeh, H. C.},
    title = {LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature},
    journal = {J Am Chem Soc},
    volume = {139},
    number = {20},
    pages = {7110-7116},
    ISSN = {1520-5126 (Electronic)
    0002-7863 (Linking)},
    DOI = {10.1021/jacs.7b03395},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28463488},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] F. Aviat, A. Levitt, B. Stamm, Y. Maday, P. Ren, J. W. Ponder, L. Lagardere, and J. P. Piquemal, “Truncated conjugate gradient: an optimal strategy for the analytical evaluation of the many-body polarization energy and forces in molecular simulations,” J chem theory comput, vol. 13, iss. 1, pp. 180-190, 2017.
    [Bibtex]
    @article{RN96,
    author = {Aviat, F. and Levitt, A. and Stamm, B. and Maday, Y. and Ren, P. and Ponder, J. W. and Lagardere, L. and Piquemal, J. P.},
    title = {Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations},
    journal = {J Chem Theory Comput},
    volume = {13},
    number = {1},
    pages = {180-190},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/acs.jctc.6b00981},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28068773},
    year = {2017},
    type = {Journal Article}
    }
  • R. Edupuganti, J. M. Taliaferro, Q. Wang, X. Xie, E. J. Cho, F. Vidhu, P. Ren, E. V. Anslyn, C. Bartholomeusz, and K. N. Dalby, “Discovery of a potent inhibitor of melk that inhibits expression of the anti-apoptotic protein mcl-1 and tnbc cell growth,” Bioorganic & medicinal chemistry, vol. 25, iss. 9, pp. 2609-2616, 2017.
    [Bibtex]
    @article{RN106,
    author = {Edupuganti, Ramakrishna and Taliaferro, Juliana M and Wang, Qiantao and Xie, Xuemei and Cho, Eun Jeong and Vidhu, Fnu and Ren, Pengyu and Anslyn, Eric V and Bartholomeusz, Chandra and Dalby, Kevin N},
    title = {Discovery of a potent inhibitor of MELK that inhibits expression of the anti-apoptotic protein Mcl-1 and TNBC cell growth},
    journal = {Bioorganic & Medicinal Chemistry},
    volume = {25},
    number = {9},
    pages = {2609-2616},
    ISSN = {0968-0896},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] M. Harger, D. Li, Z. Wang, K. Dalby, L. Lagardere, J. P. Piquemal, J. Ponder, and P. Ren, “Tinker-openmm: absolute and relative alchemical free energies using amoeba on gpus,” J comput chem, vol. 38, iss. 23, pp. 2047-2055, 2017.
    [Bibtex]
    @article{RN114,
    author = {Harger, M. and Li, D. and Wang, Z. and Dalby, K. and Lagardere, L. and Piquemal, J. P. and Ponder, J. and Ren, P.},
    title = {Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs},
    journal = {J Comput Chem},
    volume = {38},
    number = {23},
    pages = {2047-2055},
    ISSN = {1096-987X (Electronic)
    0192-8651 (Linking)},
    DOI = {10.1002/jcc.24853},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28600826},
    year = {2017},
    type = {Journal Article}
    }
  • J. A. Rackers, Q. Wang, C. Liu, J. Piquemal, P. Ren, and J. W. Ponder, “An optimized charge penetration model for use with the amoeba force field,” Physical chemistry chemical physics, vol. 19, iss. 1, pp. 276-291, 2017.
    [Bibtex]
    @article{RN104,
    author = {Rackers, Joshua A and Wang, Qiantao and Liu, Chengwen and Piquemal, Jean-Philip and Ren, Pengyu and Ponder, Jay W},
    title = {An optimized charge penetration model for use with the AMOEBA force field},
    journal = {Physical Chemistry Chemical Physics},
    volume = {19},
    number = {1},
    pages = {276-291},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] S. Deng, Q. Wang, and P. Ren, “Estimating and modeling charge transfer from the sapt induction energy,” J comput chem, vol. 38, iss. 26, pp. 2222-2231, 2017.
    [Bibtex]
    @article{RN113,
    author = {Deng, S. and Wang, Q. and Ren, P.},
    title = {Estimating and modeling charge transfer from the SAPT induction energy},
    journal = {J Comput Chem},
    volume = {38},
    number = {26},
    pages = {2222-2231},
    ISSN = {1096-987X (Electronic)
    0192-8651 (Linking)},
    DOI = {10.1002/jcc.24864},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28766729},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] C. Wang, P. Ren, and R. Luo, “Ionic solution: what goes right and wrong with continuum solvation modeling,” J phys chem b, vol. 121, iss. 49, pp. 11169-11179, 2017.
    [Bibtex]
    @article{RN133,
    author = {Wang, C. and Ren, P. and Luo, R.},
    title = {Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling},
    journal = {J Phys Chem B},
    volume = {121},
    number = {49},
    pages = {11169-11179},
    ISSN = {1520-5207 (Electronic)
    1520-5207 (Linking)},
    DOI = {10.1021/acs.jpcb.7b09616},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/29164898},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] B. S. Wendel, C. He, M. Qu, D. Wu, S. M. Hernandez, K. Y. Ma, E. W. Liu, J. Xiao, P. D. Crompton, S. K. Pierce, P. Ren, K. Chen, and N. Jiang, “Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nat commun, vol. 8, iss. 1, p. 531, 2017.
    [Bibtex]
    @article{RN116,
    author = {Wendel, B. S. and He, C. and Qu, M. and Wu, D. and Hernandez, S. M. and Ma, K. Y. and Liu, E. W. and Xiao, J. and Crompton, P. D. and Pierce, S. K. and Ren, P. and Chen, K. and Jiang, N.},
    title = {Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children},
    journal = {Nat Commun},
    volume = {8},
    number = {1},
    pages = {531},
    ISSN = {2041-1723 (Electronic)
    2041-1723 (Linking)},
    DOI = {10.1038/s41467-017-00645-x},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28912592},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] C. Zhang, D. Bell, M. Harger, and P. Ren, “Polarizable multipole-based force field for aromatic molecules and nucleobases,” J chem theory comput, vol. 13, iss. 2, pp. 666-678, 2017.
    [Bibtex]
    @article{RN105,
    author = {Zhang, C. and Bell, D. and Harger, M. and Ren, P.},
    title = {Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases},
    journal = {J Chem Theory Comput},
    volume = {13},
    number = {2},
    pages = {666-678},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/acs.jctc.6b00918},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28030769},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] D. R. Bell, S. Y. Cheng, H. Salazar, and P. Ren, “Capturing rna folding free energy with coarse-grained molecular dynamics simulations,” Sci rep, vol. 7, p. 45812, 2017.
    [Bibtex]
    @article{RN107,
    author = {Bell, D. R. and Cheng, S. Y. and Salazar, H. and Ren, P.},
    title = {Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations},
    journal = {Sci Rep},
    volume = {7},
    pages = {45812},
    ISSN = {2045-2322 (Electronic)
    2045-2322 (Linking)},
    DOI = {10.1038/srep45812},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28393861},
    year = {2017},
    type = {Journal Article}
    }
  • [DOI] X. Han, Z. Jing, W. Wu, B. Zou, Z. Peng, P. Ren, A. Wikramanayake, Z. Lu, and R. M. Leblanc, “Biocompatible and blood-brain barrier permeable carbon dots for inhibition of abeta fibrillation and toxicity, and bace1 activity,” Nanoscale, vol. 9, iss. 35, pp. 12862-12866, 2017.
    [Bibtex]
    @article{RN115,
    author = {Han, X. and Jing, Z. and Wu, W. and Zou, B. and Peng, Z. and Ren, P. and Wikramanayake, A. and Lu, Z. and Leblanc, R. M.},
    title = {Biocompatible and blood-brain barrier permeable carbon dots for inhibition of Abeta fibrillation and toxicity, and BACE1 activity},
    journal = {Nanoscale},
    volume = {9},
    number = {35},
    pages = {12862-12866},
    ISSN = {2040-3372 (Electronic)
    2040-3364 (Linking)},
    DOI = {10.1039/c7nr04352j},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/28850143},
    year = {2017},
    type = {Journal Article}
    }
  • C. Wang, P. H. Nguyen, K. Pham, D. Huynh, T. N. Le, H. Wang, P. Ren, and R. Luo, “Calculating protein–ligand binding affinities with mmpbsa: method and error analysis,” Journal of computational chemistry, vol. 37, iss. 27, pp. 2436-2446, 2016.
    [Bibtex]
    @article{RN102,
    author = {Wang, Changhao and Nguyen, Peter H and Pham, Kevin and Huynh, Danielle and Le, Thanh‐Binh Nancy and Wang, Hongli and Ren, Pengyu and Luo, Ray},
    title = {Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis},
    journal = {Journal of computational chemistry},
    volume = {37},
    number = {27},
    pages = {2436-2446},
    ISSN = {1096-987X},
    year = {2016},
    type = {Journal Article}
    }
  • C. Narth, L. Lagardère, E. Polack, N. Gresh, Q. Wang, D. R. Bell, J. A. Rackers, J. W. Ponder, P. Y. Ren, and J. Piquemal, “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, vol. 37, iss. 5, pp. 494-506, 2016.
    [Bibtex]
    @article{RN94,
    author = {Narth, Christophe and Lagardère, Louis and Polack, Etienne and Gresh, Nohad and Wang, Qiantao and Bell, David R and Rackers, Joshua A and Ponder, Jay W and Ren, Pengyu Y and Piquemal, Jean‐Philip},
    title = {Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short‐range penetration correction up to quadrupoles},
    journal = {Journal of computational chemistry},
    volume = {37},
    number = {5},
    pages = {494-506},
    ISSN = {1096-987X},
    year = {2016},
    type = {Journal Article}
    }
  • [DOI] R. Qi, Q. Wang, and P. Ren, “General van der waals potential for common organic molecules,” Bioorg med chem, vol. 24, iss. 20, pp. 4911-4919, 2016.
    [Bibtex]
    @article{RN101,
    author = {Qi, R. and Wang, Q. and Ren, P.},
    title = {General van der Waals potential for common organic molecules},
    journal = {Bioorg Med Chem},
    volume = {24},
    number = {20},
    pages = {4911-4919},
    ISSN = {1464-3391 (Electronic)
    0968-0896 (Linking)},
    DOI = {10.1016/j.bmc.2016.07.062},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/27519463},
    year = {2016},
    type = {Journal Article}
    }
  • [DOI] J. R. Houser, D. J. Busch, D. R. Bell, B. Li, P. Ren, and J. C. Stachowiak, “The impact of physiological crowding on the diffusivity of membrane bound proteins,” Soft matter, vol. 12, iss. 7, pp. 2127-34, 2016.
    [Bibtex]
    @article{RN95,
    author = {Houser, J. R. and Busch, D. J. and Bell, D. R. and Li, B. and Ren, P. and Stachowiak, J. C.},
    title = {The impact of physiological crowding on the diffusivity of membrane bound proteins},
    journal = {Soft Matter},
    volume = {12},
    number = {7},
    pages = {2127-34},
    ISSN = {1744-6848 (Electronic)
    1744-683X (Linking)},
    DOI = {10.1039/c5sm02572a},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/26751985},
    year = {2016},
    type = {Journal Article}
    }
  • D. R. Bell, R. Qi, Z. Jing, J. Y. Xiang, C. Mejias, M. J. Schnieders, J. W. Ponder, and P. Ren, “Calculating binding free energies of host–guest systems using the amoeba polarizable force field,” Physical chemistry chemical physics, vol. 18, iss. 44, pp. 30261-30269, 2016.
    [Bibtex]
    @article{RN103,
    author = {Bell, David R and Qi, Rui and Jing, Zhifeng and Xiang, Jin Yu and Mejias, Christopher and Schnieders, Michael J and Ponder, Jay W and Ren, Pengyu},
    title = {Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field},
    journal = {Physical Chemistry Chemical Physics},
    volume = {18},
    number = {44},
    pages = {30261-30269},
    year = {2016},
    type = {Journal Article}
    }
  • Q. Wang, R. Edupuganti, C. D. Tavares, K. N. Dalby, and P. Ren, “Using docking and alchemical free energy approach to determine the binding mechanism of eef2k inhibitors and prioritizing the compound synthesis,” Frontiers in molecular biosciences, vol. 2, 2015.
    [Bibtex]
    @article{RN87,
    author = {Wang, Qiantao and Edupuganti, Ramakrishna and Tavares, Clint DJ and Dalby, Kevin N and Ren, Pengyu},
    title = {Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis},
    journal = {Frontiers in molecular biosciences},
    volume = {2},
    year = {2015},
    type = {Journal Article}
    }
  • [DOI] F. Lipparini, L. Lagardere, C. Raynaud, B. Stamm, E. Cances, B. Mennucci, M. Schnieders, P. Ren, Y. Maday, and J. P. Piquemal, “Polarizable molecular dynamics in a polarizable continuum solvent,” J chem theory comput, vol. 11, iss. 2, pp. 623-34, 2015.
    [Bibtex]
    @article{RN86,
    author = {Lipparini, F. and Lagardere, L. and Raynaud, C. and Stamm, B. and Cances, E. and Mennucci, B. and Schnieders, M. and Ren, P. and Maday, Y. and Piquemal, J. P.},
    title = {Polarizable molecular dynamics in a polarizable continuum solvent},
    journal = {J Chem Theory Comput},
    volume = {11},
    number = {2},
    pages = {623-34},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/ct500998q},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/26516318},
    year = {2015},
    type = {Journal Article}
    }
  • , 2015.
    [Bibtex]
    @misc{RN89,
    volume = {28},
    pages = {51-86},
    year = {2015},
    type = {Generic}
    }
  • H. Torabifard, O. N. Starovoytov, P. Ren, and A. G. Cisneros, “Development of an amoeba water model using gem distributed multipoles,” Theoretical chemistry accounts, vol. 134, iss. 8, p. 101, 2015.
    [Bibtex]
    @article{RN92,
    author = {Torabifard, Hedieh and Starovoytov, Oleg N and Ren, Pengyu and Cisneros, G Andrés},
    title = {Development of an AMOEBA water model using GEM distributed multipoles},
    journal = {Theoretical Chemistry Accounts},
    volume = {134},
    number = {8},
    pages = {101},
    ISSN = {1432-881X},
    year = {2015},
    type = {Journal Article}
    }
  • L. Lagardère, F. Lipparini, E. Polack, B. Stamm, E. Cances, M. Schnieders, P. Ren, Y. Maday, and J. Piquemal, “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, vol. 11, iss. 6, pp. 2589-2599, 2015.
    [Bibtex]
    @article{RN90,
    author = {Lagardère, Louis and Lipparini, Filippo and Polack, Etienne and Stamm, Benjamin and Cances, Eric and Schnieders, Michael and Ren, Pengyu and Maday, Yvon and Piquemal, Jean-Philip},
    title = {Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle Mesh Ewald},
    journal = {Journal of chemical theory and computation},
    volume = {11},
    number = {6},
    pages = {2589-2599},
    ISSN = {1549-9618},
    year = {2015},
    type = {Journal Article}
    }
  • [DOI] R. Qi, L. P. Wang, Q. Wang, V. S. Pande, and P. Ren, “United polarizable multipole water model for molecular mechanics simulation,” J chem phys, vol. 143, iss. 1, p. 14504, 2015.
    [Bibtex]
    @article{RN91,
    author = {Qi, R. and Wang, L. P. and Wang, Q. and Pande, V. S. and Ren, P.},
    title = {United polarizable multipole water model for molecular mechanics simulation},
    journal = {J Chem Phys},
    volume = {143},
    number = {1},
    pages = {014504},
    ISSN = {1089-7690 (Electronic)
    0021-9606 (Linking)},
    DOI = {10.1063/1.4923338},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/26156485},
    year = {2015},
    type = {Journal Article}
    }
  • [DOI] Q. Wang, J. A. Rackers, C. He, R. Qi, C. Narth, L. Lagardere, N. Gresh, J. W. Ponder, J. P. Piquemal, and P. Ren, “General model for treating short-range electrostatic penetration in a molecular mechanics force field,” J chem theory comput, vol. 11, iss. 6, pp. 2609-2618, 2015.
    [Bibtex]
    @article{RN88,
    author = {Wang, Q. and Rackers, J. A. and He, C. and Qi, R. and Narth, C. and Lagardere, L. and Gresh, N. and Ponder, J. W. and Piquemal, J. P. and Ren, P.},
    title = {General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field},
    journal = {J Chem Theory Comput},
    volume = {11},
    number = {6},
    pages = {2609-2618},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/acs.jctc.5b00267},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/26413036},
    year = {2015},
    type = {Journal Article}
    }
  • [DOI] M. Warthaka, C. H. Adelmann, T. S. Kaoud, R. Edupuganti, C. Yan, J. Johnson W. H., S. Ferguson, C. D. Tavares, L. J. Pence, E. V. Anslyn, P. Ren, K. Y. Tsai, and K. N. Dalby, “Quantification of a pharmacodynamic erk end point in melanoma cell lysates: toward personalized precision medicine,” Acs med chem lett, vol. 6, iss. 1, pp. 47-52, 2015.
    [Bibtex]
    @article{RN85,
    author = {Warthaka, M. and Adelmann, C. H. and Kaoud, T. S. and Edupuganti, R. and Yan, C. and Johnson, W. H., Jr. and Ferguson, S. and Tavares, C. D. and Pence, L. J. and Anslyn, E. V. and Ren, P. and Tsai, K. Y. and Dalby, K. N.},
    title = {Quantification of a Pharmacodynamic ERK End Point in Melanoma Cell Lysates: Toward Personalized Precision Medicine},
    journal = {ACS Med Chem Lett},
    volume = {6},
    number = {1},
    pages = {47-52},
    ISSN = {1948-5875 (Print)
    1948-5875 (Linking)},
    DOI = {10.1021/ml500198b},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/25589929},
    year = {2015},
    type = {Journal Article}
    }
  • [DOI] C. Zhang, C. Lu, Q. Wang, J. W. Ponder, and P. Ren, “Polarizable multipole-based force field for dimethyl and trimethyl phosphate,” J chem theory comput, vol. 11, iss. 11, pp. 5326-39, 2015.
    [Bibtex]
    @article{RN93,
    author = {Zhang, C. and Lu, C. and Wang, Q. and Ponder, J. W. and Ren, P.},
    title = {Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate},
    journal = {J Chem Theory Comput},
    volume = {11},
    number = {11},
    pages = {5326-39},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/acs.jctc.5b00562},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/26574325},
    year = {2015},
    type = {Journal Article}
    }
  • [DOI] Q. Wang, J. Park, A. K. Devkota, E. J. Cho, K. N. Dalby, and P. Ren, “Identification and validation of novel perk inhibitors,” J chem inf model, vol. 54, iss. 5, pp. 1467-75, 2014.
    [Bibtex]
    @article{RN77,
    author = {Wang, Q. and Park, J. and Devkota, A. K. and Cho, E. J. and Dalby, K. N. and Ren, P.},
    title = {Identification and validation of novel PERK inhibitors},
    journal = {J Chem Inf Model},
    volume = {54},
    number = {5},
    pages = {1467-75},
    ISSN = {1549-960X (Electronic)
    1549-9596 (Linking)},
    DOI = {10.1021/ci500114r},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/24745945},
    year = {2014},
    type = {Journal Article}
    }
  • X. Mu, Q. Wang, L. Wang, S. D. Fried, J. Piquemal, K. N. Dalby, and P. Ren, “Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field,” The journal of physical chemistry b, vol. 118, iss. 24, pp. 6456-6465, 2014.
    [Bibtex]
    @article{RN75,
    author = {Mu, Xiaojiao and Wang, Qiantao and Wang, Lee-Ping and Fried, Stephen D and Piquemal, Jean-Philip and Dalby, Kevin N and Ren, Pengyu},
    title = {Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field},
    journal = {The Journal of Physical Chemistry B},
    volume = {118},
    number = {24},
    pages = {6456-6465},
    ISSN = {1520-6106},
    year = {2014},
    type = {Journal Article}
    }
  • [DOI] A. K. Devkota, R. Edupuganti, C. Yan, Y. Shi, J. Jose, Q. Wang, T. S. Kaoud, E. J. Cho, P. Ren, and K. N. Dalby, “Reversible covalent inhibition of eef-2k by carbonitriles,” Chembiochem, vol. 15, iss. 16, pp. 2435-42, 2014.
    [Bibtex]
    @article{RN83,
    author = {Devkota, A. K. and Edupuganti, R. and Yan, C. and Shi, Y. and Jose, J. and Wang, Q. and Kaoud, T. S. and Cho, E. J. and Ren, P. and Dalby, K. N.},
    title = {Reversible covalent inhibition of eEF-2K by carbonitriles},
    journal = {Chembiochem},
    volume = {15},
    number = {16},
    pages = {2435-42},
    ISSN = {1439-7633 (Electronic)
    1439-4227 (Linking)},
    DOI = {10.1002/cbic.201402321},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/25224652},
    year = {2014},
    type = {Journal Article}
    }
  • [DOI] C. D. Tavares, S. B. Ferguson, D. H. Giles, Q. Wang, R. M. Wellmann, J. P. O’Brien, M. Warthaka, J. S. Brodbelt, P. Ren, and K. N. Dalby, “The molecular mechanism of eukaryotic elongation factor 2 kinase activation,” J biol chem, vol. 289, iss. 34, pp. 23901-16, 2014.
    [Bibtex]
    @article{RN81,
    author = {Tavares, C. D. and Ferguson, S. B. and Giles, D. H. and Wang, Q. and Wellmann, R. M. and O'Brien, J. P. and Warthaka, M. and Brodbelt, J. S. and Ren, P. and Dalby, K. N.},
    title = {The molecular mechanism of eukaryotic elongation factor 2 kinase activation},
    journal = {J Biol Chem},
    volume = {289},
    number = {34},
    pages = {23901-16},
    ISSN = {1083-351X (Electronic)
    0021-9258 (Linking)},
    DOI = {10.1074/jbc.M114.577148},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/25012662},
    year = {2014},
    type = {Journal Article}
    }
  • Z. Xia, Q. Wang, X. Mu, and P. Ren, “Development of amoeba force field with advanced electrostatics,” Molecular modeling at the atomic scale: methods and applications in quantitative biology, p. 83, 2014.
    [Bibtex]
    @article{RN82,
    author = {Xia, Zhen and Wang, Qiantao and Mu, Xiaojia and Ren, Pengyu},
    title = {Development of AMOEBA Force Field with Advanced Electrostatics},
    journal = {Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology},
    pages = {83},
    ISSN = {1466562951},
    year = {2014},
    type = {Journal Article}
    }
  • K. M. Eckes, X. Mu, M. A. Ruehle, P. Ren, and L. J. Suggs, “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, vol. 30, iss. 18, pp. 5287-5296, 2014.
    [Bibtex]
    @article{RN78,
    author = {Eckes, Kevin M and Mu, Xiaojia and Ruehle, Marissa A and Ren, Pengyu and Suggs, Laura J},
    title = {β Sheets not required: Combined experimental and computational studies of self-assembly and gelation of the ester-containing analogue of an Fmoc-dipeptide hydrogelator},
    journal = {Langmuir},
    volume = {30},
    number = {18},
    pages = {5287-5296},
    ISSN = {0743-7463},
    year = {2014},
    type = {Journal Article}
    }
  • R. Edupuganti, Q. Wang, C. D. Tavares, C. A. Chitjian, J. L. Bachman, P. Ren, E. V. Anslyn, and K. N. Dalby, “Synthesis and biological evaluation of pyrido [2, 3-d] pyrimidine-2, 4-dione derivatives as eef-2k inhibitors,” Bioorganic & medicinal chemistry, vol. 22, iss. 17, pp. 4910-4916, 2014.
    [Bibtex]
    @article{RN80,
    author = {Edupuganti, Ramakrishna and Wang, Qiantao and Tavares, Clint DJ and Chitjian, Catrina A and Bachman, James L and Ren, Pengyu and Anslyn, Eric V and Dalby, Kevin N},
    title = {Synthesis and biological evaluation of pyrido [2, 3-d] pyrimidine-2, 4-dione derivatives as eEF-2K inhibitors},
    journal = {Bioorganic & medicinal chemistry},
    volume = {22},
    number = {17},
    pages = {4910-4916},
    ISSN = {0968-0896},
    year = {2014},
    type = {Journal Article}
    }
  • [DOI] G. A. Cisneros, M. Karttunen, P. Ren, and C. Sagui, “Classical electrostatics for biomolecular simulations,” Chem rev, vol. 114, iss. 1, pp. 779-814, 2014.
    [Bibtex]
    @article{RN71,
    author = {Cisneros, G. A. and Karttunen, M. and Ren, P. and Sagui, C.},
    title = {Classical electrostatics for biomolecular simulations},
    journal = {Chem Rev},
    volume = {114},
    number = {1},
    pages = {779-814},
    ISSN = {1520-6890 (Electronic)
    0009-2665 (Linking)},
    DOI = {10.1021/cr300461d},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/23981057},
    year = {2014},
    type = {Journal Article}
    }
  • H. Shen, Y. Li, P. Ren, D. Zhang, and G. Li, “Anisotropic coarse-grained model for proteins based on gay–berne and electric multipole potentials,” Journal of chemical theory and computation, vol. 10, iss. 2, pp. 731-750, 2014.
    [Bibtex]
    @article{RN74,
    author = {Shen, Hujun and Li, Yan and Ren, Pengyu and Zhang, Dinglin and Li, Guohui},
    title = {Anisotropic coarse-grained model for proteins based on Gay–Berne and electric multipole potentials},
    journal = {Journal of chemical theory and computation},
    volume = {10},
    number = {2},
    pages = {731-750},
    ISSN = {1549-9618},
    year = {2014},
    type = {Journal Article}
    }
  • [DOI] J. R. Abella, S. Y. Cheng, Q. Wang, W. Yang, and P. Ren, “Hydration free energy from orthogonal space random walk and polarizable force field,” J chem theory comput, vol. 10, iss. 7, pp. 2792-2801, 2014.
    [Bibtex]
    @article{RN79,
    author = {Abella, J. R. and Cheng, S. Y. and Wang, Q. and Yang, W. and Ren, P.},
    title = {Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field},
    journal = {J Chem Theory Comput},
    volume = {10},
    number = {7},
    pages = {2792-2801},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/ct500202q},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/25018674},
    year = {2014},
    type = {Journal Article}
    }
  • F. Lipparini, L. Lagardère, B. Stamm, E. Cancès, M. Schnieders, P. Ren, Y. Maday, and J. Piquemal, “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, vol. 10, iss. 4, pp. 1638-1651, 2014.
    [Bibtex]
    @article{RN76,
    author = {Lipparini, Filippo and Lagardère, Louis and Stamm, Benjamin and Cancès, Eric and Schnieders, Michael and Ren, Pengyu and Maday, Yvon and Piquemal, Jean-Philip},
    title = {Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: I. toward massively parallel direct space computations},
    journal = {Journal of Chemical Theory and Computation},
    volume = {10},
    number = {4},
    pages = {1638-1651},
    ISSN = {1549-9618},
    year = {2014},
    type = {Journal Article}
    }
  • [DOI] A. Marjolin, C. Gourlaouen, C. Clavaguera, P. Y. Ren, J. P. Piquemal, and J. P. Dognon, “Hydration gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics,” J mol model, vol. 20, iss. 10, p. 2471, 2014.
    [Bibtex]
    @article{RN84,
    author = {Marjolin, A. and Gourlaouen, C. and Clavaguera, C. and Ren, P. Y. and Piquemal, J. P. and Dognon, J. P.},
    title = {Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics},
    journal = {J Mol Model},
    volume = {20},
    number = {10},
    pages = {2471},
    ISSN = {0948-5023 (Electronic)
    0948-5023 (Linking)},
    DOI = {10.1007/s00894-014-2471-6},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/25296890},
    year = {2014},
    type = {Journal Article}
    }
  • [DOI] Y. Shi, Z. Xia, J. Zhang, R. Best, C. Wu, J. W. Ponder, and P. Ren, “The polarizable atomic multipole-based amoeba force field for proteins,” J chem theory comput, vol. 9, iss. 9, pp. 4046-4063, 2013.
    [Bibtex]
    @article{RN68,
    author = {Shi, Y. and Xia, Z. and Zhang, J. and Best, R. and Wu, C. and Ponder, J. W. and Ren, P.},
    title = {The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins},
    journal = {J Chem Theory Comput},
    volume = {9},
    number = {9},
    pages = {4046-4063},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/ct4003702},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/24163642},
    year = {2013},
    type = {Journal Article}
    }
  • [DOI] L. P. Wang, T. Head-Gordon, J. W. Ponder, P. Ren, J. D. Chodera, P. K. Eastman, T. J. Martinez, and V. S. Pande, “Systematic improvement of a classical molecular model of water,” J phys chem b, vol. 117, iss. 34, pp. 9956-72, 2013.
    [Bibtex]
    @article{RN67,
    author = {Wang, L. P. and Head-Gordon, T. and Ponder, J. W. and Ren, P. and Chodera, J. D. and Eastman, P. K. and Martinez, T. J. and Pande, V. S.},
    title = {Systematic improvement of a classical molecular model of water},
    journal = {J Phys Chem B},
    volume = {117},
    number = {34},
    pages = {9956-72},
    ISSN = {1520-5207 (Electronic)
    1520-5207 (Linking)},
    DOI = {10.1021/jp403802c},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/23750713},
    year = {2013},
    type = {Journal Article}
    }
  • X. Wu, Y. Shi, P. Ren, D. Wang, and G. Li, “Exploring the relationship between sequences, structures, dynamical behaviors and functions of new type protein drugs: darpins,” Current pharmaceutical design, vol. 19, iss. 12, pp. 2308-2317, 2013.
    [Bibtex]
    @article{RN60,
    author = {Wu, Xue and Shi, Yue and Ren, Pengyu and Wang, Deping and Li, Guohui},
    title = {Exploring the Relationship between Sequences, Structures, Dynamical Behaviors and Functions of New Type Protein Drugs: DARPins},
    journal = {Current pharmaceutical design},
    volume = {19},
    number = {12},
    pages = {2308-2317},
    ISSN = {1381-6128},
    year = {2013},
    type = {Journal Article}
    }
  • Z. Xia, D. R. Bell, Y. Shi, and P. Ren, “Rna 3d structure prediction by using a coarse-grained model and experimental data,” The journal of physical chemistry b, vol. 117, iss. 11, pp. 3135-3144, 2013.
    [Bibtex]
    @article{RN65,
    author = {Xia, Zhen and Bell, David R and Shi, Yue and Ren, Pengyu},
    title = {RNA 3D structure prediction by using a coarse-grained model and experimental data},
    journal = {The Journal of Physical Chemistry B},
    volume = {117},
    number = {11},
    pages = {3135-3144},
    ISSN = {1520-6106},
    year = {2013},
    type = {Journal Article}
    }
  • [DOI] D. W. Dykstra, K. N. Dalby, and P. Ren, “Elucidating binding modes of zuonin a enantiomers to jnk1 via in silico methods,” J mol graph model, vol. 45, pp. 38-44, 2013.
    [Bibtex]
    @article{RN70,
    author = {Dykstra, D. W. and Dalby, K. N. and Ren, P.},
    title = {Elucidating binding modes of zuonin A enantiomers to JNK1 via in silico methods},
    journal = {J Mol Graph Model},
    volume = {45},
    pages = {38-44},
    ISSN = {1873-4243 (Electronic)
    1093-3263 (Linking)},
    DOI = {10.1016/j.jmgm.2013.08.008},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/24001752},
    year = {2013},
    type = {Journal Article}
    }
  • [DOI] S. D. Fried, L. P. Wang, S. G. Boxer, P. Ren, and V. S. Pande, “Calculations of the electric fields in liquid solutions,” J phys chem b, vol. 117, iss. 50, pp. 16236-48, 2013.
    [Bibtex]
    @article{RN73,
    author = {Fried, S. D. and Wang, L. P. and Boxer, S. G. and Ren, P. and Pande, V. S.},
    title = {Calculations of the electric fields in liquid solutions},
    journal = {J Phys Chem B},
    volume = {117},
    number = {50},
    pages = {16236-48},
    ISSN = {1520-5207 (Electronic)
    1520-5207 (Linking)},
    DOI = {10.1021/jp410720y},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/24304155},
    year = {2013},
    type = {Journal Article}
    }
  • Z. Xia, T. Huynh, P. Ren, and R. Zhou, “Correction: large domain motions in ago protein controlled by the guide dna-strand seed region determine the ago-dna-mrna complex recognition process,” Plos one, vol. 8, iss. 8, 2013.
    [Bibtex]
    @article{RN69,
    author = {Xia, Zhen and Huynh, Tien and Ren, Pengyu and Zhou, Ruhong},
    title = {Correction: Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process},
    journal = {PloS one},
    volume = {8},
    number = {8},
    year = {2013},
    type = {Journal Article}
    }
  • Z. Xia, T. Huynh, P. Ren, and R. Zhou, “Large domain motions in ago protein controlled by the guide dna-strand seed region determine the ago-dna,” , 2013.
    [Bibtex]
    @article{RN97,
    author = {Xia, Z and Huynh, T and Ren, P and Zhou, R},
    title = {Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA},
    year = {2013},
    type = {Journal Article}
    }
  • T. Fu, H. Ren, J. Zhang, P. Ren, I. Enyedy, and G. Li, “Role of bivalent cations in structural stabilities of new drug targets—vacciniarelated kinases (vrk) from molecular dynamics simulations,” Current pharmaceutical design, vol. 19, iss. 12, pp. 2269-2281, 2013.
    [Bibtex]
    @article{RN66,
    author = {Fu, Ting and Ren, Hong and Zhang, Jiajing and Ren, Pengyu and Enyedy, Istvan and Li, Guohui},
    title = {Role of Bivalent Cations in Structural Stabilities of New Drug Targets—Vacciniarelated Kinases (VRK) from Molecular Dynamics Simulations},
    journal = {Current pharmaceutical design},
    volume = {19},
    number = {12},
    pages = {2269-2281},
    ISSN = {1381-6128},
    year = {2013},
    type = {Journal Article}
    }
  • [DOI] Z. Xia, T. Huynh, P. Ren, and R. Zhou, “Large domain motions in ago protein controlled by the guide dna-strand seed region determine the ago-dna-mrna complex recognition process,” Plos one, vol. 8, iss. 1, p. e54620, 2013.
    [Bibtex]
    @article{RN64,
    author = {Xia, Z. and Huynh, T. and Ren, P. and Zhou, R.},
    title = {Large domain motions in Ago protein controlled by the guide DNA-strand seed region determine the Ago-DNA-mRNA complex recognition process},
    journal = {PLoS One},
    volume = {8},
    number = {1},
    pages = {e54620},
    ISSN = {1932-6203 (Electronic)
    1932-6203 (Linking)},
    DOI = {10.1371/journal.pone.0054620},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/23382927},
    year = {2013},
    type = {Journal Article}
    }
  • Z. Xia and P. Ren, “Prediction and coarse-grained modeling of rna structures,” in Biophysics of rna folding, Springer new york, 2013, pp. 53-68.
    [Bibtex]
    @inbook{RN61,
    author = {Xia, Zhen and Ren, Pengyu},
    title = {Prediction and coarse-grained modeling of RNA structures},
    booktitle = {Biophysics of RNA Folding},
    publisher = {Springer New York},
    pages = {53-68},
    ISBN = {1461449537},
    year = {2013},
    type = {Book Section}
    }
  • Z. Xia, P. Clark, T. Huynh, P. Loher, Y. Zhao, H. Chen, P. Ren, I. Rigoutsos, and R. Zhou, “Erratum: molecular dynamics simulations of ago silencing complexes reveal a large repertoire of admissible’seed-less’ targets,” Scientific reports, vol. 2, 2012.
    [Bibtex]
    @article{RN63,
    author = {Xia, Zhen and Clark, Peter and Huynh, Tien and Loher, Phillipe and Zhao, Yue and Chen, Huang-Wen and Ren, Pengyu and Rigoutsos, Isidore and Zhou, Ruhong},
    title = {ERRATUM: Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible'seed-less' targets},
    journal = {Scientific reports},
    volume = {2},
    year = {2012},
    type = {Journal Article}
    }
  • R. Xiong, X. Cai, J. Wei, and P. Ren, “Some insights into the binding mechanism of aurora b kinase gained by molecular dynamics simulation,” Journal of molecular modeling, vol. 18, iss. 10, pp. 4591-4601, 2012.
    [Bibtex]
    @article{RN59,
    author = {Xiong, Rui and Cai, Xiao-Mei and Wei, Jing and Ren, Peng-Yu},
    title = {Some insights into the binding mechanism of Aurora B kinase gained by molecular dynamics simulation},
    journal = {Journal of molecular modeling},
    volume = {18},
    number = {10},
    pages = {4591-4601},
    ISSN = {1610-2940},
    year = {2012},
    type = {Journal Article}
    }
  • [DOI] J. Zhang, Y. Shi, and P. Ren, “Polarizable force fields for scoring protein-ligand interactions,” in Protein-ligand interactions, Wiley-vch verlag gmbh & co. kgaa, 2012, pp. 99-120.
    [Bibtex]
    @inbook{RN8,
    author = {Zhang, Jiajing and Shi, Yue and Ren, Pengyu},
    title = {Polarizable Force Fields for Scoring Protein-Ligand Interactions},
    booktitle = {Protein-Ligand Interactions},
    publisher = {Wiley-VCH Verlag GmbH & Co. KGaA},
    pages = {99-120},
    ISBN = {9783527645947
    9783527329663},
    DOI = {10.1002/9783527645947.ch6},
    url = {http://dx.doi.org/10.1002/9783527645947.ch6},
    year = {2012},
    type = {Book Section}
    }
  • [DOI] J. C. Wu, G. Chattree, and P. Ren, “Automation of amoeba polarizable force field parameterization for small molecules,” Theor chem acc, vol. 131, iss. 3, p. 1138, 2012.
    [Bibtex]
    @article{RN48,
    author = {Wu, J. C. and Chattree, G. and Ren, P.},
    title = {Automation of AMOEBA polarizable force field parameterization for small molecules},
    journal = {Theor Chem Acc},
    volume = {131},
    number = {3},
    pages = {1138},
    ISSN = {1432-881X (Print)
    1432-2234 (Linking)},
    DOI = {10.1007/s00214-012-1138-6},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/22505837},
    year = {2012},
    type = {Journal Article}
    }
  • [DOI] T. S. Kaoud, H. Park, S. Mitra, C. Yan, C. C. Tseng, Y. Shi, J. Jose, J. M. Taliaferro, K. Lee, P. Ren, J. Hong, and K. N. Dalby, “Manipulating jnk signaling with (–)-zuonin a,” Acs chem biol, vol. 7, iss. 11, pp. 1873-83, 2012.
    [Bibtex]
    @article{RN57,
    author = {Kaoud, T. S. and Park, H. and Mitra, S. and Yan, C. and Tseng, C. C. and Shi, Y. and Jose, J. and Taliaferro, J. M. and Lee, K. and Ren, P. and Hong, J. and Dalby, K. N.},
    title = {Manipulating JNK signaling with (--)-zuonin A},
    journal = {ACS Chem Biol},
    volume = {7},
    number = {11},
    pages = {1873-83},
    ISSN = {1554-8937 (Electronic)
    1554-8929 (Linking)},
    DOI = {10.1021/cb300261e},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/22916726},
    year = {2012},
    type = {Journal Article}
    }
  • T. S. Kaoud, C. Yan, S. Mitra, C. Tseng, J. Jose, J. M. Taliaferro, M. Tuohetahuntila, A. Devkota, R. Sammons, and J. Park, “From in silico discovery to intracellular activity: targeting jnk–protein interactions with small molecules,” Acs medicinal chemistry letters, vol. 3, iss. 9, pp. 721-725, 2012.
    [Bibtex]
    @article{RN54,
    author = {Kaoud, Tamer S and Yan, Chunli and Mitra, Shreya and Tseng, Chun-Chia and Jose, Jiney and Taliaferro, Juliana M and Tuohetahuntila, Maidina and Devkota, Ashwini and Sammons, Rachel and Park, Jihyun},
    title = {From in silico discovery to intracellular activity: targeting JNK–protein interactions with small molecules},
    journal = {ACS medicinal chemistry letters},
    volume = {3},
    number = {9},
    pages = {721-725},
    ISSN = {1948-5875},
    year = {2012},
    type = {Journal Article}
    }
  • [DOI] J. Zhang, W. Yang, J. P. Piquemal, and P. Ren, “Modeling structural coordination and ligand binding in zinc proteins with a polarizable potential,” J chem theory comput, vol. 8, iss. 4, pp. 1314-1324, 2012.
    [Bibtex]
    @article{RN58,
    author = {Zhang, J. and Yang, W. and Piquemal, J. P. and Ren, P.},
    title = {Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential},
    journal = {J Chem Theory Comput},
    volume = {8},
    number = {4},
    pages = {1314-1324},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/ct200812y},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/22754403},
    year = {2012},
    type = {Journal Article}
    }
  • [DOI] X. Mu, K. M. Eckes, M. M. Nguyen, L. J. Suggs, and P. Ren, “Experimental and computational studies reveal an alternative supramolecular structure for fmoc-dipeptide self-assembly,” Biomacromolecules, vol. 13, iss. 11, pp. 3562-71, 2012.
    [Bibtex]
    @article{RN56,
    author = {Mu, X. and Eckes, K. M. and Nguyen, M. M. and Suggs, L. J. and Ren, P.},
    title = {Experimental and computational studies reveal an alternative supramolecular structure for fmoc-dipeptide self-assembly},
    journal = {Biomacromolecules},
    volume = {13},
    number = {11},
    pages = {3562-71},
    ISSN = {1526-4602 (Electronic)
    1525-7797 (Linking)},
    DOI = {10.1021/bm301007r},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/23020140},
    year = {2012},
    type = {Journal Article}
    }
  • Y. Shi, C. Z. Zhu, S. F. Martin, and P. Ren, “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, vol. 116, iss. 5, pp. 1716-1727, 2012.
    [Bibtex]
    @article{RN52,
    author = {Shi, Yue and Zhu, Crystal Z and Martin, Stephen F and Ren, Pengyu},
    title = {Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations},
    journal = {The Journal of Physical Chemistry B},
    volume = {116},
    number = {5},
    pages = {1716-1727},
    ISSN = {1520-6106},
    year = {2012},
    type = {Journal Article}
    }
  • A. Marjolin, C. Gourlaouen, C. Clavaguéra, P. Y. Ren, J. C. Wu, N. Gresh, J. Dognon, and J. Piquemal, “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, vol. 131, iss. 4, pp. 1-14, 2012.
    [Bibtex]
    @article{RN53,
    author = {Marjolin, Aude and Gourlaouen, Christophe and Clavaguéra, Carine and Ren, Pengyu Y and Wu, Johnny C and Gresh, Nohad and Dognon, Jean-Pierre and Piquemal, Jean-Philip},
    title = {Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies},
    journal = {Theoretical Chemistry Accounts},
    volume = {131},
    number = {4},
    pages = {1-14},
    ISSN = {1432-881X},
    year = {2012},
    type = {Journal Article}
    }
  • H. Shen, Z. Xia, G. Li, and P. Ren, “A review of physics-based coarse-grained potentials for the simulations of protein structure and dynamics-chapter five,” , 2012.
    [Bibtex]
    @article{RN100,
    author = {Shen, Hujun and Xia, Zhen and Li, Guohui and Ren, Pengyu},
    title = {A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics-Chapter Five},
    year = {2012},
    type = {Journal Article}
    }
  • M. J. Schnieders, T. S. Kaoud, C. Yan, K. N. Dalby, and P. Ren, “Computational insights for the discovery of non-atp competitive inhibitors of map kinases,” Current pharmaceutical design, vol. 18, iss. 9, p. 1173, 2012.
    [Bibtex]
    @article{RN43,
    author = {J. Schnieders, Michael and S. Kaoud, Tamer and Yan, Chunli and N. Dalby, Kevin and Ren, Pengyu},
    title = {Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases},
    journal = {Current pharmaceutical design},
    volume = {18},
    number = {9},
    pages = {1173},
    ISSN = {1381-6128},
    year = {2012},
    type = {Journal Article}
    }
  • [DOI] P. Ren, J. Chun, D. G. Thomas, M. J. Schnieders, M. Marucho, J. Zhang, and N. A. Baker, “Biomolecular electrostatics and solvation: a computational perspective,” Q rev biophys, vol. 45, iss. 4, pp. 427-91, 2012.
    [Bibtex]
    @article{RN62,
    author = {Ren, P. and Chun, J. and Thomas, D. G. and Schnieders, M. J. and Marucho, M. and Zhang, J. and Baker, N. A.},
    title = {Biomolecular electrostatics and solvation: a computational perspective},
    journal = {Q Rev Biophys},
    volume = {45},
    number = {4},
    pages = {427-91},
    ISSN = {1469-8994 (Electronic)
    0033-5835 (Linking)},
    DOI = {10.1017/S003358351200011X},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/23217364},
    year = {2012},
    type = {Journal Article}
    }
  • [DOI] M. J. Schnieders, J. Baltrusaitis, Y. Shi, G. Chattree, L. Zheng, W. Yang, and P. Ren, “The structure, thermodynamics and solubility of organic crystals from simulation with a polarizable force field,” J chem theory comput, vol. 8, iss. 5, pp. 1721-1736, 2012.
    [Bibtex]
    @article{RN45,
    author = {Schnieders, M. J. and Baltrusaitis, J. and Shi, Y. and Chattree, G. and Zheng, L. and Yang, W. and Ren, P.},
    title = {The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field},
    journal = {J Chem Theory Comput},
    volume = {8},
    number = {5},
    pages = {1721-1736},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/ct300035u},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/22582032},
    year = {2012},
    type = {Journal Article}
    }
  • A. Piserchio, M. Warthaka, A. K. Devkota, T. S. Kaoud, S. Lee, O. Abramczyk, P. Ren, K. N. Dalby, and R. Ghose, “Solution nmr insights into docking interactions involving inactive erk2,” Biochemistry, vol. 50, iss. 18, pp. 3660-3672, 2011.
    [Bibtex]
    @article{RN36,
    author = {Piserchio, Andrea and Warthaka, Mangalika and Devkota, Ashwini K and Kaoud, Tamer S and Lee, Sunbae and Abramczyk, Olga and Ren, Pengyu and Dalby, Kevin N and Ghose, Ranajeet},
    title = {Solution NMR insights into docking interactions involving inactive ERK2},
    journal = {Biochemistry},
    volume = {50},
    number = {18},
    pages = {3660-3672},
    ISSN = {0006-2960},
    year = {2011},
    type = {Journal Article}
    }
  • T. Yang, J. C. Wu, C. Yan, Y. Wang, R. Luo, M. B. Gonzales, K. N. Dalby, and P. Ren, “Virtual screening using molecular simulations,” Proteins: structure, function, and bioinformatics, vol. 79, iss. 6, pp. 1940-1951, 2011.
    [Bibtex]
    @article{RN34,
    author = {Yang, Tianyi and Wu, Johnny C and Yan, Chunli and Wang, Yuanfeng and Luo, Ray and Gonzales, Michael B and Dalby, Kevin N and Ren, Pengyu},
    title = {Virtual screening using molecular simulations},
    journal = {Proteins: Structure, Function, and Bioinformatics},
    volume = {79},
    number = {6},
    pages = {1940-1951},
    ISSN = {1097-0134},
    year = {2011},
    type = {Journal Article}
    }
  • [DOI] J. Wu, X. Zhen, H. Shen, G. Li, and P. Ren, “Gay-berne and electrostatic multipole based coarse-grain potential in implicit solvent,” J chem phys, vol. 135, iss. 15, p. 155104, 2011.
    [Bibtex]
    @article{RN51,
    author = {Wu, J. and Zhen, X. and Shen, H. and Li, G. and Ren, P.},
    title = {Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent},
    journal = {J Chem Phys},
    volume = {135},
    number = {15},
    pages = {155104},
    ISSN = {1089-7690 (Electronic)
    0021-9606 (Linking)},
    DOI = {10.1063/1.3651626},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/22029338},
    year = {2011},
    type = {Journal Article}
    }
  • C. Yan, T. Kaoud, S. Lee, K. N. Dalby, and P. Ren, “Understanding the specificity of a docking interaction between jnk1 and the scaffolding protein jip1,” The journal of physical chemistry b, vol. 115, iss. 6, pp. 1491-1502, 2011.
    [Bibtex]
    @article{RN38,
    author = {Yan, Chunli and Kaoud, Tamer and Lee, Sunbae and Dalby, Kevin N and Ren, Pengyu},
    title = {Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1},
    journal = {The Journal of Physical Chemistry B},
    volume = {115},
    number = {6},
    pages = {1491-1502},
    ISSN = {1520-6106},
    year = {2011},
    type = {Journal Article}
    }
  • [DOI] P. Ren, C. Wu, and J. W. Ponder, “Polarizable atomic multipole-based molecular mechanics for organic molecules,” J chem theory comput, vol. 7, iss. 10, pp. 3143-3161, 2011.
    [Bibtex]
    @article{RN29,
    author = {Ren, P. and Wu, C. and Ponder, J. W.},
    title = {Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules},
    journal = {J Chem Theory Comput},
    volume = {7},
    number = {10},
    pages = {3143-3161},
    ISSN = {1549-9626 (Electronic)
    1549-9618 (Linking)},
    DOI = {10.1021/ct200304d},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/22022236},
    year = {2011},
    type = {Journal Article}
    }
  • [DOI] D. R. Kryscio, Y. Shi, P. Ren, and N. A. Peppas, “Molecular docking simulations for macromolecularly imprinted polymers,” Ind eng chem res, vol. 50, iss. 24, pp. 13877-13884, 2011.
    [Bibtex]
    @article{RN46,
    author = {Kryscio, D. R. and Shi, Y. and Ren, P. and Peppas, N. A.},
    title = {Molecular docking simulations for macromolecularly imprinted polymers},
    journal = {Ind Eng Chem Res},
    volume = {50},
    number = {24},
    pages = {13877-13884},
    ISSN = {0888-5885 (Print)
    0888-5885 (Linking)},
    DOI = {10.1021/ie201858n},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/22287827},
    year = {2011},
    type = {Journal Article}
    }
  • [DOI] D. P. Gardner, P. Ren, S. Ozer, and R. R. Gutell, “Statistical potentials for hairpin and internal loops improve the accuracy of the predicted rna structure,” J mol biol, vol. 413, iss. 2, pp. 473-83, 2011.
    [Bibtex]
    @article{RN50,
    author = {Gardner, D. P. and Ren, P. and Ozer, S. and Gutell, R. R.},
    title = {Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure},
    journal = {J Mol Biol},
    volume = {413},
    number = {2},
    pages = {473-83},
    ISSN = {1089-8638 (Electronic)
    0022-2836 (Linking)},
    DOI = {10.1016/j.jmb.2011.08.033},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/21889515},
    year = {2011},
    type = {Journal Article}
    }
  • S. Lee, M. Warthaka, C. Yan, T. S. Kaoud, A. Piserchio, R. Ghose, P. Ren, and K. N. Dalby, “A model of a mapk• substrate complex in an active conformation: a computational and experimental approach,” Plos one, vol. 6, iss. 4, p. e18594, 2011.
    [Bibtex]
    @article{RN40,
    author = {Lee, Sunbae and Warthaka, Mangalika and Yan, Chunli and Kaoud, Tamer S and Piserchio, Andrea and Ghose, Ranajeet and Ren, Pengyu and Dalby, Kevin N},
    title = {A model of a MAPK• substrate complex in an active conformation: A computational and experimental approach},
    journal = {PLoS One},
    volume = {6},
    number = {4},
    pages = {e18594},
    ISSN = {1932-6203},
    year = {2011},
    type = {Journal Article}
    }
  • [DOI] Y. Shi, C. Wu, J. W. Ponder, and P. Ren, “Multipole electrostatics in hydration free energy calculations,” J comput chem, vol. 32, iss. 5, pp. 967-77, 2011.
    [Bibtex]
    @article{RN31,
    author = {Shi, Y. and Wu, C. and Ponder, J. W. and Ren, P.},
    title = {Multipole electrostatics in hydration free energy calculations},
    journal = {J Comput Chem},
    volume = {32},
    number = {5},
    pages = {967-77},
    ISSN = {1096-987X (Electronic)
    0192-8651 (Linking)},
    DOI = {10.1002/jcc.21681},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/20925089},
    year = {2011},
    type = {Journal Article}
    }
  • [DOI] S. Lee, M. Warthaka, C. Yan, T. S. Kaoud, P. Ren, and K. N. Dalby, “Examining docking interactions on erk2 with modular peptide substrates,” Biochemistry, vol. 50, iss. 44, pp. 9500-10, 2011.
    [Bibtex]
    @article{RN44,
    author = {Lee, S. and Warthaka, M. and Yan, C. and Kaoud, T. S. and Ren, P. and Dalby, K. N.},
    title = {Examining docking interactions on ERK2 with modular peptide substrates},
    journal = {Biochemistry},
    volume = {50},
    number = {44},
    pages = {9500-10},
    ISSN = {1520-4995 (Electronic)
    0006-2960 (Linking)},
    DOI = {10.1021/bi201103b},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/21955038},
    year = {2011},
    type = {Journal Article}
    }
  • [DOI] J. M. Fonner, C. E. Schmidt, and P. Ren, “A combined molecular dynamics and experimental study of doped polypyrrole,” Polymer (guildf), vol. 51, iss. 21, pp. 4985-4993, 2010.
    [Bibtex]
    @article{RN49,
    author = {Fonner, J. M. and Schmidt, C. E. and Ren, P.},
    title = {A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole},
    journal = {Polymer (Guildf)},
    volume = {51},
    number = {21},
    pages = {4985-4993},
    ISSN = {0032-3861 (Print)
    0032-3861 (Linking)},
    DOI = {10.1016/j.polymer.2010.08.024},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/21052521},
    year = {2010},
    type = {Journal Article}
    }
  • J. C. Wu, J. Piquemal, R. Chaudret, P. Reinhardt, and P. Ren, “Polarizable molecular dynamics simulation of zn (ii) in water using the amoeba force field,” Journal of chemical theory and computation, vol. 6, iss. 7, pp. 2059-2070, 2010.
    [Bibtex]
    @article{RN28,
    author = {Wu, Johnny C and Piquemal, Jean-Philip and Chaudret, Robin and Reinhardt, Peter and Ren, Pengyu},
    title = {Polarizable molecular dynamics simulation of Zn (II) in water using the AMOEBA force field},
    journal = {Journal of chemical theory and computation},
    volume = {6},
    number = {7},
    pages = {2059-2070},
    ISSN = {1549-9618},
    year = {2010},
    type = {Journal Article}
    }
  • [DOI] Z. Xia, D. P. Gardner, R. R. Gutell, and P. Ren, “Coarse-grained model for simulation of rna three-dimensional structures,” J phys chem b, vol. 114, iss. 42, pp. 13497-506, 2010.
    [Bibtex]
    @article{RN37,
    author = {Xia, Z. and Gardner, D. P. and Gutell, R. R. and Ren, P.},
    title = {Coarse-grained model for simulation of RNA three-dimensional structures},
    journal = {J Phys Chem B},
    volume = {114},
    number = {42},
    pages = {13497-506},
    ISSN = {1520-5207 (Electronic)
    1520-5207 (Linking)},
    DOI = {10.1021/jp104926t},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/20883011},
    year = {2010},
    type = {Journal Article}
    }
  • [DOI] J. W. Ponder, C. Wu, P. Ren, V. S. Pande, J. D. Chodera, M. J. Schnieders, I. Haque, D. L. Mobley, D. S. Lambrecht, J. DiStasio R. A., M. Head-Gordon, G. N. Clark, M. E. Johnson, and T. Head-Gordon, “Current status of the amoeba polarizable force field,” J phys chem b, vol. 114, iss. 8, pp. 2549-64, 2010.
    [Bibtex]
    @article{RN17,
    author = {Ponder, J. W. and Wu, C. and Ren, P. and Pande, V. S. and Chodera, J. D. and Schnieders, M. J. and Haque, I. and Mobley, D. L. and Lambrecht, D. S. and DiStasio, R. A., Jr. and Head-Gordon, M. and Clark, G. N. and Johnson, M. E. and Head-Gordon, T.},
    title = {Current status of the AMOEBA polarizable force field},
    journal = {J Phys Chem B},
    volume = {114},
    number = {8},
    pages = {2549-64},
    ISSN = {1520-5207 (Electronic)
    1520-5207 (Linking)},
    DOI = {10.1021/jp910674d},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/20136072},
    year = {2010},
    type = {Journal Article}
    }
  • [DOI] K. Callaway, W. F. Waas, M. A. Rainey, P. Ren, and K. N. Dalby, “Phosphorylation of the transcription factor ets-1 by erk2: rapid dissociation of adp and phospho-ets-1,” Biochemistry, vol. 49, iss. 17, pp. 3619-30, 2010.
    [Bibtex]
    @article{RN35,
    author = {Callaway, K. and Waas, W. F. and Rainey, M. A. and Ren, P. and Dalby, K. N.},
    title = {Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1},
    journal = {Biochemistry},
    volume = {49},
    number = {17},
    pages = {3619-30},
    ISSN = {1520-4995 (Electronic)
    0006-2960 (Linking)},
    DOI = {10.1021/bi100199q},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/20361728},
    year = {2010},
    type = {Journal Article}
    }
  • [DOI] J. Zhang, C. A. King, K. Dalby, and P. Ren, “Conformational preference of chak1 binding peptides: a molecular dynamics study,” Pmc biophys, vol. 3, iss. 1, p. 2, 2010.
    [Bibtex]
    @article{RN47,
    author = {Zhang, J. and King, C. A. and Dalby, K. and Ren, P.},
    title = {Conformational preference of ChaK1 binding peptides: a molecular dynamics study},
    journal = {PMC Biophys},
    volume = {3},
    number = {1},
    pages = {2},
    ISSN = {1757-5036 (Electronic)
    1757-5036 (Linking)},
    DOI = {10.1186/1757-5036-3-2},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/20180991},
    year = {2010},
    type = {Journal Article}
    }
  • [DOI] C. Yan, V. Pattani, J. W. Tunnell, and P. Ren, “Temperature-induced unfolding of epidermal growth factor (egf): insight from molecular dynamics simulation,” J mol graph model, vol. 29, iss. 1, pp. 2-12, 2010.
    [Bibtex]
    @article{RN41,
    author = {Yan, C. and Pattani, V. and Tunnell, J. W. and Ren, P.},
    title = {Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation},
    journal = {J Mol Graph Model},
    volume = {29},
    number = {1},
    pages = {2-12},
    ISSN = {1873-4243 (Electronic)
    1093-3263 (Linking)},
    DOI = {10.1016/j.jmgm.2010.03.011},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/20466569},
    year = {2010},
    type = {Journal Article}
    }
  • [DOI] J. C. Wu, D. P. Gardner, S. Ozer, R. R. Gutell, and P. Ren, “Correlation of rna secondary structure statistics with thermodynamic stability and applications to folding,” J mol biol, vol. 391, iss. 4, pp. 769-83, 2009.
    [Bibtex]
    @article{RN32,
    author = {Wu, J. C. and Gardner, D. P. and Ozer, S. and Gutell, R. R. and Ren, P.},
    title = {Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding},
    journal = {J Mol Biol},
    volume = {391},
    number = {4},
    pages = {769-83},
    ISSN = {1089-8638 (Electronic)
    0022-2836 (Linking)},
    DOI = {10.1016/j.jmb.2009.06.036},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/19540243},
    year = {2009},
    type = {Journal Article}
    }
  • [DOI] D. Jiao, J. Zhang, R. E. Duke, G. Li, M. J. Schnieders, and P. Ren, “Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential,” J comput chem, vol. 30, iss. 11, pp. 1701-11, 2009.
    [Bibtex]
    @article{RN27,
    author = {Jiao, D. and Zhang, J. and Duke, R. E. and Li, G. and Schnieders, M. J. and Ren, P.},
    title = {Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential},
    journal = {J Comput Chem},
    volume = {30},
    number = {11},
    pages = {1701-11},
    ISSN = {1096-987X (Electronic)
    0192-8651 (Linking)},
    DOI = {10.1002/jcc.21268},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/19399779},
    year = {2009},
    type = {Journal Article}
    }
  • D. Jiao, P. A. Golubkov, T. A. Darden, and P. Ren, “Calculation of protein–ligand binding free energy by using a polarizable potential,” Proceedings of the national academy of sciences, vol. 105, iss. 17, pp. 6290-6295, 2008.
    [Bibtex]
    @article{RN19,
    author = {Jiao, Dian and Golubkov, Pavel A and Darden, Thomas A and Ren, Pengyu},
    title = {Calculation of protein–ligand binding free energy by using a polarizable potential},
    journal = {Proceedings of the National Academy of Sciences},
    volume = {105},
    number = {17},
    pages = {6290-6295},
    ISSN = {0027-8424},
    year = {2008},
    type = {Journal Article}
    }
  • [DOI] P. A. Golubkov, J. C. Wu, and P. Ren, “A transferable coarse-grained model for hydrogen-bonding liquids,” Phys chem chem phys, vol. 10, iss. 15, pp. 2050-7, 2008.
    [Bibtex]
    @article{RN33,
    author = {Golubkov, P. A. and Wu, J. C. and Ren, P.},
    title = {A transferable coarse-grained model for hydrogen-bonding liquids},
    journal = {Phys Chem Chem Phys},
    volume = {10},
    number = {15},
    pages = {2050-7},
    ISSN = {1463-9076 (Print)
    1463-9076 (Linking)},
    DOI = {10.1039/b715841f},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/18688358},
    year = {2008},
    type = {Journal Article}
    }
  • [DOI] H. X. Li, B. Y. Hwang, G. Laxmikanthan, S. I. Blaber, M. Blaber, P. A. Golubkov, P. Ren, B. L. Iverson, and G. Georgiou, “Substrate specificity of human kallikreins 1 and 6 determined by phage display,” Protein sci, vol. 17, iss. 4, pp. 664-72, 2008.
    [Bibtex]
    @article{RN30,
    author = {Li, H. X. and Hwang, B. Y. and Laxmikanthan, G. and Blaber, S. I. and Blaber, M. and Golubkov, P. A. and Ren, P. and Iverson, B. L. and Georgiou, G.},
    title = {Substrate specificity of human kallikreins 1 and 6 determined by phage display},
    journal = {Protein Sci},
    volume = {17},
    number = {4},
    pages = {664-72},
    ISSN = {1469-896X (Electronic)
    0961-8368 (Linking)},
    DOI = {10.1110/ps.073333208},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/18359858},
    year = {2008},
    type = {Journal Article}
    }
  • T. D. Rasmussen, P. Ren, J. W. Ponder, and F. Jensen, “Force field modeling of conformational energies: importance of multipole moments and intramolecular polarization,” International journal of quantum chemistry, vol. 107, iss. 6, pp. 1390-1395, 2007.
    [Bibtex]
    @article{RN24,
    author = {Rasmussen, Thomas D and Ren, Pengyu and Ponder, Jay W and Jensen, Frank},
    title = {Force field modeling of conformational energies: importance of multipole moments and intramolecular polarization},
    journal = {International Journal of Quantum Chemistry},
    volume = {107},
    number = {6},
    pages = {1390-1395},
    ISSN = {1097-461X},
    year = {2007},
    type = {Journal Article}
    }
  • [DOI] M. J. Schnieders, N. A. Baker, P. Ren, and J. W. Ponder, “Polarizable atomic multipole solutes in a poisson-boltzmann continuum,” J chem phys, vol. 126, iss. 12, p. 124114, 2007.
    [Bibtex]
    @article{RN23,
    author = {Schnieders, M. J. and Baker, N. A. and Ren, P. and Ponder, J. W.},
    title = {Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum},
    journal = {J Chem Phys},
    volume = {126},
    number = {12},
    pages = {124114},
    ISSN = {0021-9606 (Print)
    0021-9606 (Linking)},
    DOI = {10.1063/1.2714528},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/17411115},
    year = {2007},
    type = {Journal Article}
    }
  • [DOI] J. Zhang, M. King, L. Suggs, and P. Ren, “Molecular modeling of conformational properties of oligodepsipeptides,” Biomacromolecules, vol. 8, iss. 10, pp. 3015-24, 2007.
    [Bibtex]
    @article{RN39,
    author = {Zhang, J. and King, M. and Suggs, L. and Ren, P.},
    title = {Molecular modeling of conformational properties of oligodepsipeptides},
    journal = {Biomacromolecules},
    volume = {8},
    number = {10},
    pages = {3015-24},
    ISSN = {1525-7797 (Print)
    1525-7797 (Linking)},
    DOI = {10.1021/bm070244c},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/17877396},
    year = {2007},
    type = {Journal Article}
    }
  • [DOI] P. A. Golubkov and P. Ren, “Generalized coarse-grained model based on point multipole and gay-berne potentials,” J chem phys, vol. 125, iss. 6, p. 64103, 2006.
    [Bibtex]
    @article{RN26,
    author = {Golubkov, P. A. and Ren, P.},
    title = {Generalized coarse-grained model based on point multipole and Gay-Berne potentials},
    journal = {J Chem Phys},
    volume = {125},
    number = {6},
    pages = {64103},
    ISSN = {0021-9606 (Print)
    0021-9606 (Linking)},
    DOI = {10.1063/1.2244553},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/16942269},
    year = {2006},
    type = {Journal Article}
    }
  • D. Jiao, C. King, A. Grossfield, T. A. Darden, and P. Ren, “Simulation of ca2+ and mg2+ solvation using polarizable atomic multipole potential,” The journal of physical chemistry b, vol. 110, iss. 37, pp. 18553-18559, 2006.
    [Bibtex]
    @article{RN21,
    author = {Jiao, Dian and King, Christopher and Grossfield, Alan and Darden, Thomas A and Ren, Pengyu},
    title = {Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential},
    journal = {The Journal of Physical Chemistry B},
    volume = {110},
    number = {37},
    pages = {18553-18559},
    ISSN = {1520-6106},
    year = {2006},
    type = {Journal Article}
    }
  • J. Piquemal, L. Perera, A. G. Cisneros, P. Ren, L. G. Pedersen, and T. A. Darden, “Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: from energetics to structure,” The journal of chemical physics, vol. 125, iss. 5, p. 54511, 2006.
    [Bibtex]
    @article{RN20,
    author = {Piquemal, Jean-Philip and Perera, Lalith and Cisneros, G Andrés and Ren, Pengyu and Pedersen, Lee G and Darden, Thomas A},
    title = {Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure},
    journal = {The Journal of chemical physics},
    volume = {125},
    number = {5},
    pages = {054511},
    ISSN = {0021-9606},
    year = {2006},
    type = {Journal Article}
    }
  • P. Ren and J. W. Ponder, “Temperature and pressure dependence of the amoeba water model,” The journal of physical chemistry b, vol. 108, iss. 35, pp. 13427-13437, 2004.
    [Bibtex]
    @article{RN18,
    author = {Ren, Pengyu and Ponder, Jay W},
    title = {Temperature and pressure dependence of the AMOEBA water model},
    journal = {The Journal of Physical Chemistry B},
    volume = {108},
    number = {35},
    pages = {13427-13437},
    ISSN = {1520-6106},
    year = {2004},
    type = {Journal Article}
    }
  • [DOI] A. Grossfield, P. Ren, and J. W. Ponder, “Ion solvation thermodynamics from simulation with a polarizable force field,” J am chem soc, vol. 125, iss. 50, pp. 15671-82, 2003.
    [Bibtex]
    @article{RN16,
    author = {Grossfield, A. and Ren, P. and Ponder, J. W.},
    title = {Ion solvation thermodynamics from simulation with a polarizable force field},
    journal = {J Am Chem Soc},
    volume = {125},
    number = {50},
    pages = {15671-82},
    ISSN = {0002-7863 (Print)
    0002-7863 (Linking)},
    DOI = {10.1021/ja037005r},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/14664617},
    year = {2003},
    type = {Journal Article}
    }
  • [DOI] P. Y. Ren and J. W. Ponder, “Polarizable atomic multipole water model for molecular mechanics simulation,” Journal of physical chemistry b, vol. 107, iss. 24, pp. 5933-5947, 2003.
    [Bibtex]
    @article{RN13,
    author = {Ren, P. Y. and Ponder, J. W.},
    title = {Polarizable atomic multipole water model for molecular mechanics simulation},
    journal = {Journal of Physical Chemistry B},
    volume = {107},
    number = {24},
    pages = {5933-5947},
    ISSN = {1520-6106},
    DOI = {10.1021/jp027815+},
    url = {://WOS:000183592000039},
    year = {2003},
    type = {Journal Article}
    }
  • [DOI] P. Ren and J. W. Ponder, “Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations,” J comput chem, vol. 23, iss. 16, pp. 1497-506, 2002.
    [Bibtex]
    @article{RN15,
    author = {Ren, P. and Ponder, J. W.},
    title = {Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations},
    journal = {J Comput Chem},
    volume = {23},
    number = {16},
    pages = {1497-506},
    ISSN = {0192-8651 (Print)
    0192-8651 (Linking)},
    DOI = {10.1002/jcc.10127},
    url = {https://www.ncbi.nlm.nih.gov/pubmed/12395419},
    year = {2002},
    type = {Journal Article}
    }
  • J. Fried and P. Ren, “The atomistic simulation of the gas permeability of poly (organophosphazenes). part 1. poly (dibutoxyphosphazenes),” Computational and theoretical polymer science, vol. 10, iss. 5, pp. 447-463, 2000.
    [Bibtex]
    @article{RN25,
    author = {Fried, JR and Ren, P},
    title = {The atomistic simulation of the gas permeability of poly (organophosphazenes). Part 1. Poly (dibutoxyphosphazenes)},
    journal = {Computational and Theoretical Polymer Science},
    volume = {10},
    number = {5},
    pages = {447-463},
    ISSN = {1089-3156},
    year = {2000},
    type = {Journal Article}
    }
  • J. Fried and P. Ren, “Molecular simulation of the glass transition of polyphosphazenes,” Computational and theoretical polymer science, vol. 9, iss. 2, pp. 111-116, 1999.
    [Bibtex]
    @article{RN22,
    author = {Fried, JR and Ren, P},
    title = {Molecular simulation of the glass transition of polyphosphazenes},
    journal = {Computational and Theoretical Polymer Science},
    volume = {9},
    number = {2},
    pages = {111-116},
    ISSN = {1089-3156},
    year = {1999},
    type = {Journal Article}
    }
  • H. Sun, P. Ren, and J. Fried, “The compass force field: parameterization and validation for phosphazenes,” Computational and theoretical polymer science, vol. 8, iss. 1, pp. 229-246, 1998.
    [Bibtex]
    @article{RN14,
    author = {Sun, H and Ren, P and Fried, JR},
    title = {The COMPASS force field: parameterization and validation for phosphazenes},
    journal = {Computational and Theoretical Polymer Science},
    volume = {8},
    number = {1},
    pages = {229-246},
    ISSN = {1089-3156},
    year = {1998},
    type = {Journal Article}
    }
  • D. R. Bell, Z. Xia, and P. Ren, “Multiscale modeling of rna 3d structures,” in Biomedical sciences and engineering conference (bsec), 2013, , pp. 1-4.
    [Bibtex]
    @inproceedings{RN72,
    author = {Bell, David R and Xia, Zhen and Ren, Pengyu},
    title = {Multiscale modeling of RNA 3D structures},
    booktitle = {Biomedical Sciences and Engineering Conference (BSEC), 2013},
    publisher = {IEEE},
    pages = {1-4},
    ISBN = {1479921181},
    type = {Conference Proceedings}
    }
  • Y. Shi, D. Jiao, M. J. Schnieders, and P. Ren, “Trypsin-ligand binding free energy calculation with amoeba,” in Engineering in medicine and biology society, 2009. embc 2009. annual international conference of the ieee, , pp. 2328-2331.
    [Bibtex]
    @inproceedings{RN42,
    author = {Shi, Yue and Jiao, Dian and Schnieders, Michael J and Ren, Pengyu},
    title = {Trypsin-ligand binding free energy calculation with AMOEBA},
    booktitle = {Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE},
    publisher = {IEEE},
    pages = {2328-2331},
    ISBN = {1424432960},
    type = {Conference Proceedings}
    }