Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. - Pengyu Y. Ren; Jay W. Ponder (J. Comput. Chem., 2002)

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 Y. Ren (J. Comput. Chem., 2009)

Multipole electrostatics in hydration free energy calculations. - Yue Shi; Chuanjie Wu; Jay W. Ponder; Pengyu Y. Ren (J. Comput. Chem., 2011)

Identification and Validation of Novel PERK Inhibitors. - Qiantao Wang; Jihyun Park; Ashwini K. Devkota; Eun Jeong Cho; Kevin N. Dalby; Pengyu Y. Ren (J. Chem. Inf. Model., 2014)

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. - Christophe Narth; Louis Lagardère; Étienne Polack; Nohad Gresh; Qiantao Wang; David R. Bell; Joshua A. Rackers; Jay W. Ponder; Pengyu Y. Ren; Jean-Philip Piquemal (J. Comput. Chem., 2016)

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. - Changhao Wang; Peter H. Nguyen; Kevin Pham; Danielle Huynh; Thanh-Binh Nancy Le; Hongli Wang; Pengyu Y. Ren; Ray Luo 001 (J. Comput. Chem., 2016)

Estimating and modeling charge transfer from the SAPT induction energy. - Shi Deng; Qiantao Wang; Pengyu Y. Ren (J. Comput. Chem., 2017)

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. - Matthew Harger; Daniel Li; Zhi Wang 021; Kevin N. Dalby; Louis Lagardère; Jean-Philip Piquemal; Jay W. Ponder; Pengyu Y. Ren (J. Comput. Chem., 2017)

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0]. - Luc-Henri Jolly; Alejandro Duran; Louis Lagardère; Jay W. Ponder; Pengyu Y. Ren; Jean-Philip Piquemal (CoRR, 2019)

Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. - Olivier Adjoua; Louis Lagardère; Luc-Henri Jolly; Arnaud Durocher; Thibaut Very; Isabelle Dupays; Zhi Wang 021; Théo Jaffrelot Inizan; Frédéric Célerse; Pengyu Y. Ren; Jay W. Ponder; Jean-Philip Piquemal (CoRR, 2020)

Three-site and five-site fixed-charge water models compatible with AMOEBA force field. - Cong Pan 003; Chengwen Liu; Junhui Peng; Pengyu Y. Ren; Xuhui Huang (J. Comput. Chem., 2020)

Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition. - Zhifeng Jing; Chengwen Liu; Pengyu Y. Ren (J. Chem. Inf. Model., 2021)

E2EDNA: Simulation Protocol for DNA Aptamers with Ligands. - Michael Kilgour; Tao Liu; Brandon D. Walker; Pengyu Y. Ren; Lena Simine (J. Chem. Inf. Model., 2021)

Hydration of divalent lanthanides, Sm2+ and Eu2+: A molecular dynamics study with polarizable AMOEBA force field. - Hesam Arabzadeh; Chengwen Liu; Orlando Acevedo; Pengyu Y. Ren; Wei Yang; Thomas Albrecht-Schönzart (J. Comput. Chem., 2022)

Automation of AMOEBA polarizable force field for small molecules: Poltype 2. - Brandon D. Walker; Chengwen Liu; Elizabeth Wait; Pengyu Y. Ren (J. Comput. Chem., 2022)

Atomic Polarizabilities for Interactive Dipole Induction Models. - Jacob M. Litman; Chengwen Liu; Pengyu Y. Ren (J. Chem. Inf. Model., 2022)

Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. - Yazdan Maghsoud; Erik Antonio Vázquez-Montelongo; Xudong Yang; Chengwen Liu; Zhifeng Jing; Juhoon Lee; Matthew Harger; Ally K. Smith; Miguel Espinoza; Hou-Fu Guo; Jonathan M. Kurie; Kevin N. Dalby; et al. (J. Chem. Inf. Model., 2023)