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13 results in Authors: Pengyu Ren

Theoretical and Computational Chemistry

Working Paper

Incorporating Neural Networks into the AMOEBA Polarizable Force Field

Yanxing Wang, Théo Jaffrelot Inizan, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren

Version 3 posted 14 December 2023

1,030

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Theoretical and Computational Chemistry

Working Paper

Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field

Andrew Thiel, Matthew Speranza, Sanika Jadhav, Lewis Stevens, Daniel Unruh, Pengyu Ren, Jay Ponder, Jana Shen, Michael Schnieders

Version 1 posted 18 October 2023

347

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Theoretical and Computational Chemistry

Working Paper

Computational Investigation of a Series of Small Molecules as Lead 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, Pengyu Ren, G. Andrés Cisneros

Version 1 posted 01 September 2022

252

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Theoretical and Computational Chemistry

Working Paper

Targeting RNA with Small Molecules using State-of-the-Art Methods Provides Highly Predictive Affinities of Riboswitch Inhibitors

Narjes Ansari, Chengwen Liu, Florent Hedin, Jérôme Hénin, Jay W. Ponder, Pengyu Ren, Jean-Philip Piquemal, Louis Lagardère, Krystel El Hage

Version 2 posted 28 October 2024

931

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Citations

Theoretical and Computational Chemistry

Working Paper

A Generalized Kirkwood Implicit Solvent for the Polarizable AMOEBA Protein Model

Rae Corrigan, Andrew Thiel, Jack Lynn, Thomas Casavant, Pengyu Ren, Jay Ponder, Michael Schnieders

Version 2 posted 26 May 2023

380

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Theoretical and Computational Chemistry

Working Paper

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Rae Corrigan, Guowei Qi, Andrew Thiel, Jack Lynn, Brandon Walker, Thomas Casavant, Louis Lagardère, Jean-Philip Piquemal, Jay Ponder, Pengyu Ren, Michael Schnieders

Version 1 posted 17 December 2020

982

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Physical Chemistry

Working Paper

AMOEBA+ Classical Potential for Modeling Molecular Interactions

Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren

Version 3 posted 15 May 2019

1,698

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Biological and Medicinal Chemistry

Working Paper

Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations

Léa El Khoury, Frédéric Célerse, Louis Lagardere, Luc-Henri Jolly, Étienne Derat, Zeina Hobaika, Richard G. Maroun, Pengyu Ren, Serge Bouaziz, Nohad Gresh, Jean-Philip Piquemal

Version 3 posted 28 February 2020

977

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Theoretical and Computational Chemistry

Working Paper

Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface

Dina El Ahdab, Louis Lagardère, Theo Jaffrelot Inizan, Frédéric Célerse, Chengwen Liu, Olivier Adjoua, Luc-Henri Jolly, Nohad Gresh, Zeina Hobaika, Pengyu Ren, Richard G. Maroun, Jean-Philip Piquemal

Version 2 posted 02 June 2021

615

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Theoretical and Computational Chemistry

Working Paper

Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren

Version 1 posted 13 December 2019

510

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13 results in Pengyu Ren in Authors: Pengyu Ren

Incorporating Neural Networks into the AMOEBA Polarizable Force Field

Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field

Computational Investigation of a Series of Small Molecules as Lead Compounds for Lysyl hydroxylase-2 (LH2) Inhibition

Targeting RNA with Small Molecules using State-of-the-Art Methods Provides Highly Predictive Affinities of Riboswitch Inhibitors

A Generalized Kirkwood Implicit Solvent for the Polarizable AMOEBA Protein Model

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

AMOEBA+ Classical Potential for Modeling Molecular Interactions

Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations

Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface

Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

13 results in Authors: Pengyu Ren