Pengyu Ren

ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 51

Top Venues

The journal of physical chemistry. B

Journal of chemical theory and computation

Journal of chemical information and modeling

Molecules (Basel, Switzerland)

University of Texas at Austin

Zhejiang University (BSC)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Texas at Austin Sep 01 2005

United States

Professor :: BME

Washington University in Saint Louis School of Medicine

United States

Research Associate :: Biochemistry and Molecular Biophysics

Education History

Zhejiang University Sep 01 1989 - Jun 01 1993

China

BSC :: Chemical Engineering

Publications

Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation (2024)
Yanxing Wang, Théo Jaffrelot Inizan, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren
Incorporating Neural Networks into the AMOEBA Polarizable Force Field. The journal of physical chemistry. B (2024)
Xudong Yang, Chengwen Liu, Pengyu Ren
Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning. Journal of chemical theory and computation 20 (10) (2024)
Xudong Yang, Chengwen Liu, Pengyu Ren
Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning. Journal of chemical theory and computation (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. The Journal of chemical physics 161 (1) (2024)
Yanxing Wang, Théo Jaffrelot Inizan, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren
Incorporating Neural Networks into the AMOEBA Polarizable Force Field. The journal of physical chemistry. B 128 (10) (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. The Journal of chemical physics 161 (1) (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Yanxing Wang, Théo Jaffrelot Inizan, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren
Incorporating Neural Networks into the AMOEBA Polarizable Force Field. The journal of physical chemistry. B 128 (10) (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. The Journal of chemical physics 161 (1) (2024)
Xudong Yang, Chengwen Liu, Pengyu Ren
Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning. Journal of chemical theory and computation 20 (10) (2024)
Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng F Jing, Juhoon Lee, Matthew Harger, Ally K Smith, Miguel Espinoza, Hou-Fu Guo, Jonathan M Kurie, Kevin N Dalby, Pengyu Ren, Gerardo Andrés Cisneros
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. Journal of chemical information and modeling 63 (3) (2023)
Elizabeth E Wait, Justin Gourary, Chengwen Liu, Erik D Spoerke, Susan L B Rempe, Pengyu Ren
Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. The journal of physical chemistry. B 127 (6) (2023)
Rae A Corrigan, Andrew C Thiel, Jack R Lynn, Thomas L Casavant, Pengyu Ren, Jay W Ponder, Michael J Schnieders
A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. The Journal of chemical physics 159 (5) (2023)
Elizabeth E Wait, Justin Gourary, Chengwen Liu, Erik D Spoerke, Susan L B Rempe, Pengyu Ren
Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. The journal of physical chemistry. B 127 (6) (2023)
Elizabeth E Wait, Justin Gourary, Chengwen Liu, Erik D Spoerke, Susan L B Rempe, Pengyu Ren
Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. The journal of physical chemistry. B 127 (6) (2023)
Elizabeth E Wait, Justin Gourary, Chengwen Liu, Erik D Spoerke, Susan L B Rempe, Pengyu Ren
Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. The journal of physical chemistry. B 127 (6) (2023)
Juhoon Lee, Hou-Fu Guo, Shike Wang, Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Zhifeng F Jing, Rae M Sammons, Eun Jeong Cho, Pengyu Ren, Gerardo Andrés Cisneros, Jonathan M Kurie, Kevin N Dalby
Unleashing the Potential of 1,3-Diketone Analogues as Selective LH2 Inhibitors. ACS medicinal chemistry letters 14 (10) (2023)
Elizabeth E Wait, Justin Gourary, Chengwen Liu, Erik D Spoerke, Susan L B Rempe, Pengyu Ren
Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. The journal of physical chemistry. B (2023)
Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng F Jing, Juhoon Lee, Matthew Harger, Ally K Smith, Miguel Espinoza, Hou-Fu Guo, Jonathan M Kurie, Kevin N Dalby, Pengyu Ren, Gerardo Andrés Cisneros
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. Journal of chemical information and modeling 63 (3) (2023)
Yu-Chun Lin, Pengyu Ren, Lauren J Webb
AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies. The journal of physical chemistry. B (2023)
Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng F Jing, Juhoon Lee, Matthew Harger, Ally K Smith, Miguel Espinoza, Hou-Fu Guo, Jonathan M Kurie, Kevin N Dalby, Pengyu Ren, Gerardo Andrés Cisneros
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. Journal of chemical information and modeling 63 (3) (2023)
Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng F Jing, Juhoon Lee, Matthew Harger, Ally K Smith, Miguel Espinoza, Hou-Fu Guo, Jonathan M Kurie, Kevin N Dalby, Pengyu Ren, Gerardo Andrés Cisneros
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. Journal of chemical information and modeling 63 (3) (2023)
Sehr Naseem-Khan, Louis Lagardère, Christophe Narth, Gerardo Andrés Cisneros, Pengyu Ren, Nohad Gresh, Jean-Philip Piquemal
Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. Journal of chemical theory and computation 18 (6) (2022)
Yanxing Wang, Brandon Duane Walker, Chengwen Liu, Pengyu Ren
An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules (Basel, Switzerland) 27 (23) (2022)
Yanxing Wang, Brandon Duane Walker, Chengwen Liu, Pengyu Ren
An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules (Basel, Switzerland) 27 (23) (2022)
Hesam Arabzadeh, Brandon Walker, Joseph M Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E Albrecht Schmitt
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. The journal of physical chemistry. B 126 (50) (2022)
Hesam Arabzadeh, Brandon Walker, Joseph M Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E Albrecht Schmitt
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. The journal of physical chemistry. B (2022)
Yanxing Wang, Brandon Duane Walker, Chengwen Liu, Pengyu Ren
An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules (Basel, Switzerland) 27 (23) (2022)
Hesam Arabzadeh, Brandon Walker, Joseph M Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E Albrecht Schmitt
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. The journal of physical chemistry. B 126 (50) (2022)
Hesam Arabzadeh, Brandon Walker, Joseph M Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E Albrecht Schmitt
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. The journal of physical chemistry. B 126 (50) (2022)
Zhifeng F Jing, Pengyu Ren
Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model. The journal of physical chemistry. B 126 (38) (2022)
Hesam Arabzadeh, Brandon Walker, Joseph M Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E Albrecht Schmitt
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. The journal of physical chemistry. B 126 (50) (2022)
Hesam Arabzadeh, Brandon Walker, Joseph M Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E Albrecht Schmitt
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. The journal of physical chemistry. B 126 (50) (2022)
Hesam Arabzadeh, Brandon Walker, Joseph M Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E Albrecht Schmitt
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. The journal of physical chemistry. B 126 (50) (2022)
Yanxing Wang, Brandon Duane Walker, Chengwen Liu, Pengyu Ren
An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules (Basel, Switzerland) 27 (23) (2022)
Yanxing Wang, Brandon Duane Walker, Chengwen Liu, Pengyu Ren
An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules (Basel, Switzerland) 27 (23) (2022)
Hesam Arabzadeh, Brandon Walker, Joseph M Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E Albrecht Schmitt
Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+ , Eu 2+ , Dy 2+ , Yb 2+ , Cf 2+ , and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. The journal of physical chemistry. B 126 (50) (2022)
Michael Kilgour, Tao Liu, Brandon D Walker, Pengyu Ren, Lena Simine
E2EDNA: Simulation Protocol for DNA Aptamers with Ligands. Journal of chemical information and modeling 61 (9) (2021)
Zhifeng F Jing, Chengwen Liu, Pengyu Ren
Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition. Journal of chemical information and modeling 61 (6) (2021)
Rae A Corrigan, Guowei Qi, Andrew C Thiel, Jack R Lynn, Brandon D Walker, Thomas L Casavant, Louis Lagardere, Jean-Philip Piquemal, Jay W Ponder, Pengyu Ren, Michael J Schnieders
Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 17 (4) (2021)
Jacob M Litman, Chengwen Liu, Pengyu Ren
Atomic Polarizabilities for Interactive Dipole Induction Models. Journal of chemical information and modeling 62 (1) (2021)
Dina El Ahdab, Louis Lagardère, Théo Jaffrelot Inizan, Fréderic Célerse, Chengwen Liu, Olivier Adjoua, Luc-Henri Jolly, Nohad Gresh, Zeina Hobaika, Pengyu Ren, Richard G Maroun, Jean-Philip Piquemal
Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface. The journal of physical chemistry letters 12 (26) (2021)
Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher, Thibaut Very, Isabelle Dupays, Zhi Wang, Théo Jaffrelot Inizan, Fréderic Célerse, Pengyu 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-GPU Systems. Journal of chemical theory and computation 17 (4) (2021)
Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren
Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential. The journal of physical chemistry letters 11 (2) (2019)
Ernest Y Lee, Changsheng Zhang, Jeremy Di Domizio, Fan Jin, Will Connell, Mandy Hung, Nicolas Malkoff, Veronica Veksler, Michel Gilliet, Pengyu Ren, Gerard C L Wong
Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsDNA to TLR9. Nature communications 10 (1) (2019)
Tamer S Kaoud, William H Johnson, Nancy Danielle Ebelt, Andrea Piserchio, Diana Zamora-Olivares, Sabrina X Van Ravenstein, Jacey R Pridgen, Ramakrishna Edupuganti, Rachel M Sammons, Micael Cano, Mangalika Warthaka, Matthew Harger, Clint D J Tavares, Jihyun Park, Mohamed F Radwan, Pengyu Ren, Eric V Anslyn, Kenneth Y Tsai, Ranajeet Ghose, Kevin N Dalby
Modulating multi-functional ERK complexes by covalent targeting of a recruitment site in vivo. Nature communications 10 (1) (2019)

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Publication Activity (10 Years)

Top Topics

Top Venues

Pengyu Ren