List of works - Pengyu Ren

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

scientific article

A Model of a MAPK•Substrate Complex in an Active Conformation: A Computational and Experimental Approach ⬇️

scientific article published on April 11, 2011

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

scientific article published on 13 February 2018

Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children

scientific article published on 14 September 2017

An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.

scientific article

An optimized charge penetration model for use with the AMOEBA force field.

scientific article

Biocompatible and blood-brain barrier permeable carbon dots for inhibition of Aβ fibrillation and toxicity, and BACE1 activity.

scientific article published on 29 August 2017

Biomolecular electrostatics and solvation: a computational perspective

scientific article

Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field

scientific article published on 2 June 2016

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis

scientific article

Calculation of protein-ligand binding free energy by using a polarizable potential

scholarly article

Capturing Many-Body Interactions with Classical Dipole Induction Models

scientific article

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

scientific article

Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations

scientific article published on 16 May 2022

Elucidating binding modes of zuonin A enantiomers to JNK1 via in silico methods

scientific article published on 16 August 2013

Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution.

scientific article published on 11 June 2018

Estimating and modeling charge transfer from the SAPT induction energy

scientific article

Examining Docking Interactions on ERK2 with Modular Peptide Substrates ⬇️

scientific article published on October 18, 2011

Experimental and computational studies reveal an alternative supramolecular structure for fmoc-dipeptide self-assembly.

scientific article

Exploring the Relationship between Sequences, Structures, Dynamical Behaviors and Functions of New Type Protein Drugs: DARPins ⬇️

scientific article published on January 1, 2013

From in Silico Discovery to intra-Cellular Activity: Targeting JNK-Protein Interactions with Small Molecules ⬇️

scientific article published on August 6, 2012

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field.

scientific article

Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsDNA to TLR9

scientific article published on 04 March 2019

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.

scientific article

Identification and validation of novel PERK inhibitors

scientific article

Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential

scientific article published on 30 December 2019

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

scientific article published on 26 March 2021

Investigating the Association Mechanism between Rafoxanide and Povidone

scientific article published on 09 November 2018

LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature.

scientific article

Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process ⬇️

scientific article published on January 29, 2013

Manipulating JNK signaling with (--)-zuonin A.

scientific article published on 30 August 2012

Many-body effect determines the selectivity for Ca and Mg in proteins

article published in the Proceedings of the National Academy of Sciences of the United States of America

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential ⬇️

scientific article published on January 2, 2012

Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field

scientific article

Modulating multi-functional ERK complexes by covalent targeting of a recruitment site in vivo

scientific article published on 19 November 2019

Molecular Docking Simulations for Macromolecularly Imprinted Polymers ⬇️

scientific article published on October 31, 2011

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.

scientific article

Molecular modeling of conformational properties of oligodepsipeptides

scientific article published on 18 September 2007

Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1.

scientific article

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

scientific article

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field ⬇️

scientific article published on July 13, 2010

Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases.

scientific article published on 28 December 2016

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate.

scientific article published on 28 October 2015

Polarizable molecular dynamics in a polarizable continuum solvent

scientific article published on 26 January 2015

Reversible covalent inhibition of eEF-2K by carbonitriles.

scientific article

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald ⬇️

scientific article

Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald.

scientific article published on June 2015

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles

scientific article published on February 2016

Solution NMR insights into docking interactions involving inactive ERK2

scientific article

Some insights into the binding mechanism of Aurora B kinase gained by molecular dynamics simulation

scientific article published on 30 May 2012

Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure.

scientific article published on 23 August 2011

Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field.

scientific article published in October 2017

Synthesis and biological evaluation of pyrido[2,3-d]pyrimidine-2,4-dione derivatives as eEF-2K inhibitors.

scientific article

Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation ⬇️

scientific article

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

scientific article

The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.

scientific article

The impact of physiological crowding on the diffusivity of membrane bound proteins.

scientific article

The molecular mechanism of eukaryotic elongation factor 2 kinase activation

scientific article (publication date: 22 August 2014)

Tinker 8: Software Tools for Molecular Design

scientific article published on 19 September 2018

Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

scientific article published on 23 March 2021

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

scientific article

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

scientific article published on 10 June 2017

Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations

scientific article published on 08 December 2016

β sheets not required: combined experimental and computational studies of self-assembly and gelation of the ester-containing analogue of an Fmoc-dipeptide hydrogelator.

scientific article

List of works by Pengyu Ren

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

A Model of a MAPK•Substrate Complex in an Active Conformation: A Computational and Experimental Approach ⬇️

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children

An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.

An optimized charge penetration model for use with the AMOEBA force field.

Biocompatible and blood-brain barrier permeable carbon dots for inhibition of Aβ fibrillation and toxicity, and BACE1 activity.

Biomolecular electrostatics and solvation: a computational perspective

Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis

Calculation of protein-ligand binding free energy by using a polarizable potential

Capturing Many-Body Interactions with Classical Dipole Induction Models

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations

Elucidating binding modes of zuonin A enantiomers to JNK1 via in silico methods

Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution.

Estimating and modeling charge transfer from the SAPT induction energy

Examining Docking Interactions on ERK2 with Modular Peptide Substrates ⬇️

Experimental and computational studies reveal an alternative supramolecular structure for fmoc-dipeptide self-assembly.

Exploring the Relationship between Sequences, Structures, Dynamical Behaviors and Functions of New Type Protein Drugs: DARPins ⬇️

From in Silico Discovery to intra-Cellular Activity: Targeting JNK-Protein Interactions with Small Molecules ⬇️

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field.

Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsDNA to TLR9

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.

Identification and validation of novel PERK inhibitors

Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Investigating the Association Mechanism between Rafoxanide and Povidone

LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature.

Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process ⬇️

Manipulating JNK signaling with (--)-zuonin A.

Many-body effect determines the selectivity for Ca and Mg in proteins

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential ⬇️

Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field

Modulating multi-functional ERK complexes by covalent targeting of a recruitment site in vivo

Molecular Docking Simulations for Macromolecularly Imprinted Polymers ⬇️

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.

Molecular modeling of conformational properties of oligodepsipeptides

Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1.

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field ⬇️

Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases.

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate.

Polarizable molecular dynamics in a polarizable continuum solvent

Reversible covalent inhibition of eEF-2K by carbonitriles.

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald ⬇️

Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald.

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles

Solution NMR insights into docking interactions involving inactive ERK2

Some insights into the binding mechanism of Aurora B kinase gained by molecular dynamics simulation

Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure.

Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field.

Synthesis and biological evaluation of pyrido[2,3-d]pyrimidine-2,4-dione derivatives as eEF-2K inhibitors.

Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation ⬇️

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.

The impact of physiological crowding on the diffusivity of membrane bound proteins.

The molecular mechanism of eukaryotic elongation factor 2 kinase activation

Tinker 8: Software Tools for Molecular Design

Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations

β sheets not required: combined experimental and computational studies of self-assembly and gelation of the ester-containing analogue of an Fmoc-dipeptide hydrogelator.