Pengyu Y. Ren

Publication Activity (10 Years)

Years Active: 2002-2023
Publications (10 Years): 12

Top Topics

Median Filtering

Complex Systems

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

Publications

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
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. J. Chem. Inf. Model. 63 (3) (2023)
Jacob M. Litman, Chengwen Liu, Pengyu Y. Ren
Atomic Polarizabilities for Interactive Dipole Induction Models. J. Chem. Inf. Model. 62 (1) (2022)
Brandon D. Walker, Chengwen Liu, Elizabeth Wait, Pengyu Y. Ren
Automation of AMOEBA polarizable force field for small molecules: Poltype 2. J. Comput. Chem. 43 (23) (2022)
Zhifeng Jing, Chengwen Liu, Pengyu Y. Ren
Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition. J. Chem. Inf. Model. 61 (6) (2021)
Michael Kilgour, Tao Liu, Brandon D. Walker, Pengyu Y. Ren, Lena Simine
E2EDNA: Simulation Protocol for DNA Aptamers with Ligands. J. Chem. Inf. Model. 61 (9) (2021)
Cong Pan, Chengwen Liu, Junhui Peng, Pengyu Y. Ren, Xuhui Huang
Three-site and five-site fixed-charge water models compatible with AMOEBA force field. J. Comput. Chem. 41 (10) (2020)
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
Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. CoRR (2020)
Luc-Henri Jolly, Alejandro Duran, Louis Lagardère, Jay W. Ponder, Pengyu Y. Ren, Jean-Philip Piquemal
Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0]. CoRR (2019)
Shi Deng, Qiantao Wang, Pengyu Y. Ren
Estimating and modeling charge transfer from the SAPT induction energy. J. Comput. Chem. 38 (26) (2017)
Matthew Harger, Daniel Li, Zhi Wang, Kevin N. Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Y. Ren
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. J. Comput. Chem. 38 (23) (2017)
Changhao Wang, Peter H. Nguyen, Kevin Pham, Danielle Huynh, Thanh-Binh Nancy Le, Hongli Wang, Pengyu Y. Ren, Ray Luo
Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. J. Comput. Chem. 37 (27) (2016)
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
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. J. Comput. Chem. 37 (5) (2016)
Qiantao Wang, Jihyun Park, Ashwini K. Devkota, Eun Jeong Cho, Kevin N. Dalby, Pengyu Y. Ren
Identification and Validation of Novel PERK Inhibitors. J. Chem. Inf. Model. 54 (5) (2014)
Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Y. Ren
Multipole electrostatics in hydration free energy calculations. J. Comput. Chem. 32 (5) (2011)
Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Y. Ren
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J. Comput. Chem. 30 (11) (2009)
Pengyu Y. Ren, Jay W. Ponder
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. 23 (16) (2002)