Pengyu Y. Ren

Orcid: 0000-0002-5613-1910

Affiliations:
  • University of Texas at Austin, Department of Biomedical Engineering, USA


According to our database1, Pengyu Y. Ren authored at least 17 papers between 2002 and 2023.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.

Timeline

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Bibliography

2023
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition.
J. Chem. Inf. Model., February, 2023

2022
Atomic Polarizabilities for Interactive Dipole Induction Models.
J. Chem. Inf. Model., 2022

Automation of AMOEBA polarizable force field for small molecules: Poltype 2.
J. Comput. Chem., 2022

Hydration of divalent lanthanides, Sm2+ and Eu2+: A molecular dynamics study with polarizable AMOEBA force field.
J. Comput. Chem., 2022

2021
E2EDNA: Simulation Protocol for DNA Aptamers with Ligands.
J. Chem. Inf. Model., 2021

Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition.
J. Chem. Inf. Model., 2021

2020
Three-site and five-site fixed-charge water models compatible with AMOEBA force field.
J. Comput. Chem., 2020

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

2019
Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0].
CoRR, 2019

2017
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.
J. Comput. Chem., 2017

Estimating and modeling charge transfer from the SAPT induction energy.
J. Comput. Chem., 2017

2016
Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis.
J. Comput. Chem., 2016

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.
J. Comput. Chem., 2016

2014
Identification and Validation of Novel PERK Inhibitors.
J. Chem. Inf. Model., 2014

2011
Multipole electrostatics in hydration free energy calculations.
J. Comput. Chem., 2011

2009
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.
J. Comput. Chem., 2009

2002
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations.
J. Comput. Chem., 2002


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