Pengyu Y. Ren - RankMe

17 papers Journal 17

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. J. Chem. Inf. Model. 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, Pengyu Y. Ren, G. Andrés Cisneros
2022	J	`jnl`	Atomic Polarizabilities for Interactive Dipole Induction Models. J. Chem. Inf. Model. Jacob M. Litman, Chengwen Liu, Pengyu Y. Ren
2022	J	`jnl`	Automation of AMOEBA polarizable force field for small molecules: Poltype 2. J. Comput. Chem. Brandon D. Walker, Chengwen Liu, Elizabeth Wait, Pengyu Y. Ren
2022	J	`jnl`	Hydration of divalent lanthanides, Sm2+ and Eu2+: A molecular dynamics study with polarizable AMOEBA force field. J. Comput. Chem. Hesam Arabzadeh, Chengwen Liu, Orlando Acevedo, Pengyu Y. Ren, Wei Yang, Thomas Albrecht-Schönzart
2021	J	`jnl`	Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition. J. Chem. Inf. Model. Zhifeng Jing, Chengwen Liu, Pengyu Y. Ren
2021	J	`jnl`	E2EDNA: Simulation Protocol for DNA Aptamers with Ligands. J. Chem. Inf. Model. Michael Kilgour, Tao Liu, Brandon D. Walker, Pengyu Y. Ren, Lena Simine
2020	J	`jnl`	Three-site and five-site fixed-charge water models compatible with AMOEBA force field. J. Comput. Chem. Cong Pan, Chengwen Liu, Junhui Peng, Pengyu Y. Ren, Xuhui Huang
2020	J	`jnl`	Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. CoRR Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher, Thibaut Very, Isabelle Dupays, Zhi Wang, Théo Jaffrelot Inizan, Frédéric Célerse, Pengyu Y. Ren, Jay W. Ponder, Jean-Philip Piquemal
2019	J	`jnl`	Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0]. CoRR Luc-Henri Jolly, Alejandro Duran, Louis Lagardère, Jay W. Ponder, Pengyu Y. Ren, Jean-Philip Piquemal
2017	J	`jnl`	Estimating and modeling charge transfer from the SAPT induction energy. J. Comput. Chem. Shi Deng, Qiantao Wang, Pengyu Y. Ren
2017	J	`jnl`	Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. J. Comput. Chem. Matthew Harger, Daniel Li, Zhi Wang, Kevin N. Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Y. Ren
2016	J	`jnl`	Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. J. Comput. Chem. Changhao Wang, Peter H. Nguyen, Kevin Pham, Danielle Huynh, Thanh-Binh Nancy Le, Hongli Wang, Pengyu Y. Ren, Ray Luo
2016	J	`jnl`	Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. J. Comput. Chem. 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
2014	J	`jnl`	Identification and Validation of Novel PERK Inhibitors. J. Chem. Inf. Model. Qiantao Wang, Jihyun Park, Ashwini K. Devkota, Eun Jeong Cho, Kevin N. Dalby, Pengyu Y. Ren
2011	J	`jnl`	Multipole electrostatics in hydration free energy calculations. J. Comput. Chem. Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Y. Ren
2009	J	`jnl`	Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J. Comput. Chem. Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Y. Ren
2002	J	`jnl`	Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. Pengyu Y. Ren, Jay W. Ponder