Pengyu Ren

ORCID: 0000-0002-5613-1910

Biochemistry, Genetics and Molecular BiologyPhysics and Astronomy

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 43 papers. Top paper: “Recent progress in general force fields of small molecules”.

Recent progress in general force fields of small molecules

Current Opinion in Structural Biology(2021)10.1016/j.sbi.2021.11.011

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0.606DataRank · unranked

56 citations

Brandon Walker, Viet Hoang Man, Pengyu Ren, Junmei Wang, Xibing He

Simulations reveal a balance between protein–protein and protein–lipid interactions during condensation on membrane surfaces

Chemical Science(2025)10.1039/d5sc04862a

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0.241DataRank · unranked

4 citations

Yohan Lee, Shireen Pathak, Nishi Patel, Jeanne C. Stachowiak, Pengyu Ren +1 more

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

UNC Libraries(2020)10.17615/dj4t-jz49

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0DataRank · unranked

2 citations

Guohui Li, Michael J. Schnieders, Robert E. Duke, Dian Jiao, Jiajing Zhang +1 more

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

ChemRxiv(2020)10.26434/chemrxiv.13003166

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0DataRank · unranked

8 citations

Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu +7 more

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

ChemRxiv(2020)10.26434/chemrxiv.13003166.v5

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0DataRank · unranked

3 citations

Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu +7 more

Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.13.381897

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0DataRank · unranked

2 citations

Chengwen Liu, Martin J. Fossat, Pengyu Ren, Ashutosh Chilkoti, Rohit V. Pappu +1 more

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

ChemRxiv(2020)10.26434/chemrxiv.13003166.v3

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0DataRank · unranked

2 citations

Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henry Jolly, Chengwen Liu +7 more

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

ChemRxiv(2020)10.26434/chemrxiv.13003166.v4

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0DataRank · unranked

2 citations

Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu +7 more

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

ChemRxiv(2020)10.26434/chemrxiv.13003166.v2

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0DataRank · unranked

0 citations

Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henry Jolly, Chengwen Liu +7 more

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

ChemRxiv(2020)10.26434/chemrxiv.11336975.v2

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0DataRank · unranked

0 citations

Frédéric Célerse, Louis Lagardère, Luc-Henri Jolly, Étienne Derat, Zeina Hobaika +6 more

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

ChemRxiv(2020)10.26434/chemrxiv.13003166.v1

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0DataRank · unranked

0 citations

Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henry Jolly, Chengwen Liu +7 more

Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures

APL Materials(2021)10.1063/5.0037438

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0DataRank · unranked

58 citations

Chengwen Liu, Martin J. Fossat, Pengyu Ren, Ashutosh Chilkoti, Rohit V. Pappu +1 more

High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

Chemical Science(2021)10.1039/d1sc00145k

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0DataRank · unranked

56 citations

Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu +7 more

Thermodynamics of ion binding and occupancy in potassium channels

Chemical Science(2021)10.1039/d1sc01887f

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0DataRank · unranked

50 citations

Joshua A. Rackers, Lawrence R. Pratt, Chengwen Liu, Susan B. Rempe, Pengyu Ren +1 more

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

ChemRxiv(2021)10.26434/chemrxiv.13003166.v6

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0DataRank · unranked

1 citations

Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc-Henri Jolly, Chengwen Liu +7 more

Automation of AMOEBA polarizable force field for small molecules: Poltype 2

Journal of Computational Chemistry(2022)10.1002/jcc.26954

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0DataRank · unranked

62 citations

Chengwen Liu, Elizabeth Wait, Pengyu Ren, Brandon Walker

Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA

Frontiers in Molecular Biosciences(2022)10.3389/fmolb.2022.946708

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0DataRank · unranked

5 citations

Chengwen Liu, Yu-An Kuo, Hsin‐Chih Yeh, Pengyu Ren, Xudong Yang

AMOEBA Force Field Trajectories Improve Predictions of Accurate pKa Values of the GFP Fluorophore: The Importance of Polarizability and Water Interactions

The Journal of Physical Chemistry B(2022)10.1021/acs.jpcb.2c03642

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0DataRank · unranked

11 citations

Pengyu Ren, Lauren J. Webb, Yu-Chun Lin

An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules

Molecules(2022)10.3390/molecules27238567

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0DataRank · unranked

9 citations

Brandon Walker, Chengwen Liu, Pengyu Ren, Yanxing Wang

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

ChemRxiv(2022)10.26434/chemrxiv-2022-t2c5c

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0DataRank · unranked

2 citations

Hou‐Fu Guo, Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Zhifeng Jing, Shike Wang +7 more

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

ChemRxiv(2022)10.26434/chemrxiv-2022-dszd3

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0DataRank · unranked

1 citations

Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng Jing, Juhoon Lee +9 more

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

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.2c01448

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0DataRank · unranked

14 citations

Erik Antonio Vázquez-Montelongo, Xudong Yang, Chengwen Liu, Zhifeng Jing, Juhoon Lee +9 more

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)10.1021/acs.jpcb.3c02060

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0DataRank · unranked

11 citations

Pengyu Ren, Lauren J. Webb, Yu-Chun Lin

Unleashing the Potential of 1,3-Diketone Analogues as Selective LH2 Inhibitors

ACS Medicinal Chemistry Letters(2023)10.1021/acsmedchemlett.3c00305

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0DataRank · unranked

8 citations

Hou‐Fu Guo, Shike Wang, Yazdan Maghsoud, Erik Antonio Vázquez-Montelongo, Zhifeng Jing +7 more

A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model

The Journal of Chemical Physics(2023)10.1063/5.0158914

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0DataRank · unranked

4 citations

Andrew Thiel, Jack R. Lynn, Thomas L. Casavant, Pengyu Ren, Jay W. Ponder +2 more

Incorporating Neural Networks into the AMOEBA Polarizable Force Field

ChemRxiv(2023)10.26434/chemrxiv-2023-kgfpg

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0DataRank · unranked

2 citations

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

Incorporating Neural Networks into the AMOEBA Polarizable Force Field

ChemRxiv(2023)10.26434/chemrxiv-2023-kgfpg-v2

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0DataRank · unranked

2 citations

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

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

ChemRxiv(2023)10.26434/chemrxiv-2023-96z34

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0DataRank · unranked

1 citations

Matthew J. Speranza, Sanika Jadhav, Lewis L. Stevens, Daniel K. Unruh, Pengyu Ren +4 more

A Generalized Kirkwood Implicit Solvent for the Polarizable AMOEBA Protein Model

ChemRxiv(2023)10.26434/chemrxiv-2023-cbb38

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0DataRank · unranked

0 citations

Andrew Thiel, J. D. Lynn, Thomas L. Casavant, Pengyu Ren, Jay W. Ponder +2 more

A Generalized Kirkwood Implicit Solvent for the Polarizable AMOEBA Protein Model

ChemRxiv(2023)10.26434/chemrxiv-2023-cbb38-v2

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0DataRank · unranked

0 citations

Andrew Thiel, J. D. Lynn, Thomas L. Casavant, Pengyu Ren, Jay W. Ponder +2 more

Incorporating Neural Networks into the AMOEBA Polarizable Force Field

ChemRxiv(2023)10.26434/chemrxiv-2023-kgfpg-v3

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0DataRank · unranked

0 citations

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

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

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.3c01180

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0DataRank · unranked

17 citations

Matthew J. Speranza, Sanika Jadhav, Lewis L. Stevens, Daniel K. Unruh, Pengyu Ren +4 more

Incorporating Neural Networks into the AMOEBA Polarizable Force Field

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.3c08166

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0DataRank · unranked

11 citations

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

Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments

Molecules(2024)10.3390/molecules29143258

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0DataRank · unranked

5 citations

Elizabeth Wait, Pengyu Ren, Mayar Tarek Ibrahim

Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00053

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0DataRank · unranked

5 citations

Chengwen Liu, Pengyu Ren, Xudong Yang

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

The Journal of Chemical Physics(2024)10.1063/5.0214652

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0DataRank · unranked

1 citations

Aaron J. Nessler, Andrew Thiel, Hernan V. Bernabe, Rae Corrigan, Leah M. Cousineau +16 more

Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.07.602435

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0DataRank · unranked

2 citations

Yuan-I Chen, Yanxing Wang, Zeynep Korkmaz, Siem Yonas, Yujie He +13 more

Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotides Fragments

Preprints.org(2024)10.20944/preprints202406.0349.v1

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0DataRank · unranked

1 citations

Elizabeth Wait, Pengyu Ren, Mayar Tarek Ibrahim

Loading causes molecular damage in fibrin fibers

Soft Matter(2025)10.1039/d5sm00681c

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0DataRank · unranked

2 citations

Matthew J. Lohr, Mayar T. Ibrahim, Christian M. Jennings, Daniel Wang, Pengyu Ren +3 more

Loading causes molecular damage in fibrin fibers

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.08.652948

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0DataRank · unranked

0 citations

Matthew J. Lohr, Mayar T. Ibrahim, Christian M. Jennings, Daniel Wang, Pengyu Ren +3 more

Molecular dynamics free energy simulations of ATP:Mg2+ and ADP:Mg2+ using the polarisable force field AMOEBA

Molecular Simulation(2020)10.1080/08927022.2020.1725003

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0DataRank · unranked

15 citations

Zhifeng Jing, Pengyu Ren, Brandon Walker

Insights into fibrinogen mechanics under cyclic high-strain loading

Biophysical Journal(2025)10.1016/j.bpj.2025.11.017

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0DataRank · unranked

0 citations

Sajjad Norouzi, Uma Paul, Sapun H. Parekh, Pengyu Ren, Mayar Tarek Ibrahim

Accurate description of molecular dipole surface with charge flux implemented for molecular mechanics

The Journal of Chemical Physics(2020)10.1063/5.0016376

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0DataRank · unranked

8 citations

Chengwen Liu, Brandon Walker, Pengyu Ren, Xudong Yang