J. C. Wu, D. Gardner, S. Ozer, R. R. Gutell and P. Y. Ren, Structure Statistics with Thermodynamic Stability and Applications to Folding J. Mol. Biol. 391, 769–783 (2009) DOI Fulltext

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential, Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Ren J Comput Chem, 30, p1701-11 (2009) DOI 10.1002/jcc.21268

Calculation of Protein-Ligand Binding Free Energy Using a Polarizable Potential, D. Jiao, P.A. Golubkov, T. Darden, P. Ren, Proc  Natl Acad Sci USA  105 (17): 6290 (2008) DOI Fulltext

Substrate specificity of human kallikreins 1 and 6 determined by phage display, Hai-Xin Li1,7, Bum-Yeol Hwang1,2,7, Gurunathan Laxmikanthan3, Sachiko I. Blaber3, Michael Blaber3, Pavel A. Golubkov4, Pengyu Ren4, Brent L. Iverson1,5, and George Georgiou. Protein Science (2008 ), 17:664-672

A transferable coarse-grained model for hydrogen-bonding liquids , Pavel A. Golubkov, Johnny C. Wu and Pengyu Ren, Phys. Chem. Chem. Phys. , 10, 2050 - 2057 2008. DOI: 10.1039/b715841f

Jiajing Zhang, Michael King, Laura Suggs, and Pengyu Ren, Molecular Modeling of Conformational Properties of Oligodepsipeptides, Biomacromolecules , 8 , 3015-3024, 2007

Michael Schnieders, N. Baker, P. Ren, J.W. Ponder, Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum J. Chem. Phys . 126 , 124114, 2007

T.D. Rasmussen, P. Ren, J.W. Ponder, and F. Jensen, Force Field Modeling of Conformational Energies. The Importance of Multipole Moments and Intramolecular Polarization. Int. J. Quant. Chem. Vol 107, pages 1390-1395 2006

D. Jiao, C. King, A. Grossfield, T. Darden and P. Ren, Simulation of Mg2+ and Ca2+ Solvation using Polarizable Atomic Multipole Model, J. Phys. Chem. B. 110(37); 18553-18559 2006 . (AMOEBA Ca/Mg parameters for this calculation )

P. Golubkov, P. Ren, A generalized Coarse-Grain Model Based on Gay-Berne Function and Point Multipole Expansion, J. Chem. Phys . 125, 064103 2006 (parameters )

J.-P. Piquemal, L. Perea, G.A. Cisneros, P. Ren, L.G. Pedersen, T.A. Darden, Towards accurate solvation dynamics of divalent cations in water using the polarizable AMOEBA force field: from energetics to structure, J. Chem. Phys. 125, 054511 (2006 )

P. Ren and J. W. Ponder, Polarizable Atomic Multipole Based AMOEBA Potential for Protein Modeling (submitted)

P. Ren and J. W. Ponder, Polarizable Atomic Multipole Based Intermolecular Potential for Small Organic Molecules (submitted)

A. Grossfield, P. Ren and J. W. Ponder, Conformational Preferences of the Solvated Alanine Dipeptide from Simulations with A Polarizable Force Field (in preparation)

P. Ren and J. W. Ponder, “Temperature and Pressure Dependence of AMOEBA Water Model”, J. Phys. Chem. B 108(35), 13427-13437 (2004)

A. Grossfield, P. Ren and J. W. Ponder, Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field, J. Am. Chem. Soc. 125, 15671-15682 (2003)

P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation, J. Phys. Chem. B 107, 5933-5947 (2003)

P. Ren and J. W. Ponder, A Consistent Treatment of Intra- and Intermolecular Polarization in Molecular Mechanics Calculations, J. Comp. Chem. 23, 1497-1506 (2002)

J. R. Fried and P. Ren, The Atomistic Simulation of Gas Permeability of Poly(organophosphazenes) Part 1. Poly(dibutoxyphosphazenes), Comput. & Theor. Polym. Sci. 10, 447 (2000)

J. R. Fried and P. Ren, Molecular Simulation of the Glass Transition of Polyphosphazenes, Comput. & Theor. Polym. Sci. 9, 111 (1999)

H. Sun, P. Ren and J. R. Fried, The COMPASS Force Field: Parameterization and Validation for Phosphazenes, Comput. & Theor. Polym. Sci. 8, 229 (1998)