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ORCIDPengyu Y. Ren
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- affiliation: University of Texas at Austin, Department of Biomedical Engineering, USA
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2020 – today
- 2023
[j15]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): 986-1001 (2023)- 2022
- [j14]Hesam Arabzadeh, Chengwen Liu, Orlando Acevedo, Pengyu Y. Ren, Wei Yang, Thomas Albrecht-Schönzart:
Hydration of divalent lanthanides, Sm2+ and Eu2+: A molecular dynamics study with polarizable AMOEBA force field. J. Comput. Chem. 43(19): 1286-1297 (2022) - [j13]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): 1530-1542 (2022) - [j12]Jacob M. Litman, Chengwen Liu, Pengyu Y. Ren:
Atomic Polarizabilities for Interactive Dipole Induction Models. J. Chem. Inf. Model. 62(1): 79-87 (2022) - 2021
- [j11]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): 2806-2817 (2021) - [j10]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): 4139-4144 (2021) - 2020
- [j9]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): 1034-1044 (2020) - [i2]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 abs/2011.01207 (2020)
2010 – 2019
- 2019
- [i1]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 abs/1906.01211 (2019) - 2017
- [j8]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): 2047-2055 (2017) - [j7]Shi Deng, Qiantao Wang, Pengyu Y. Ren:
Estimating and modeling charge transfer from the SAPT induction energy. J. Comput. Chem. 38(26): 2222-2231 (2017) - 2016
- [j6]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): 494-506 (2016) - [j5]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): 2436-2446 (2016) - 2014
- [j4]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): 1467-1475 (2014) - 2011
- [j3]Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Y. Ren:
Multipole electrostatics in hydration free energy calculations. J. Comput. Chem. 32(5): 967-977 (2011)
2000 – 2009
- 2009
- [j2]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): 1701-1711 (2009) - 2002
- [j1]Pengyu Y. Ren, Jay W. Ponder:
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. 23(16): 1497-1506 (2002)
Coauthor Index
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