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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

83

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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

148

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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

244

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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

299

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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

53

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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

305

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Biological and Medicinal Chemistry

Working Paper

1,3-diketone analogs as selective lysyl hydroxylase 2 (LH2) antagonists

Juhoon Lee, Hou-fu Guo, Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Zhifeng Jing, Shike Wang, Rachel M. Sammons, Eun Jeong Cho, Pengyu Ren, G. Andrés Cisneros, Jonathan M. Kurie, Kevin N. Dalby

103

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1

Citations

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

99

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Physical Chemistry

Working Paper

AMOEBA+ Classical Potential for Modeling Molecular Interactions

Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren

227

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9 results in Pengyu Ren in Authors: Pengyu Ren

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

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

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

E2EDNA: Simulation Protocol for DNA Aptamers with Ligands

Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

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

1,3-diketone analogs as selective lysyl hydroxylase 2 (LH2) antagonists

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

AMOEBA+ Classical Potential for Modeling Molecular Interactions

9 results in Authors: Pengyu Ren