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Physical Chemistry

Working Paper

AMOEBA+ Classical Potential for Modeling Molecular Interactions

Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren

1,413

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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

489

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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

441

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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

824

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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

326

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Theoretical and Computational Chemistry

Working Paper

E2EDNA: Simulation Protocol for DNA Aptamers with Ligands

Michael Kilgour, Tao Liu, Brandon Walker, Pengyu Ren, Lena Simine

246

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Theoretical and Computational Chemistry

Working Paper

High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling

Theo Jaffrelot Inizan, Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu, Pengyu Ren, Matthieu Montes, Nathalie Lagarde, Louis Lagardère, Pierre Monmarché, Jean-Philip Piquemal

1,732

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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

80

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8 results in Pengyu Ren in Authors: Pengyu Ren

AMOEBA+ Classical Potential for Modeling Molecular Interactions

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Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

View abstract keyboard_arrow_down

Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

View abstract keyboard_arrow_down

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

View abstract keyboard_arrow_down

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

View abstract keyboard_arrow_down

E2EDNA: Simulation Protocol for DNA Aptamers with Ligands

View abstract keyboard_arrow_down

High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling

View abstract keyboard_arrow_down

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

View abstract keyboard_arrow_down

8 results in Authors: Pengyu Ren