Lista de obras - Pengyu Ren - Dominio Público Uruguay

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

artículo científico publicado en 2010

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

artículo científico publicado el 11 de abril de 2011

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

artículo científico publicado en 2018

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

Biomolecular electrostatics and solvation: a computational perspective

artículo científico publicado en 2012

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

artículo científico publicado en 2016

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

artículo científico publicado en 2016

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

artículo científico publicado en 2008

Capturing Many-Body Interactions with Classical Dipole Induction Models

artículo científico publicado en 2017

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

artículo científico publicado en 2009

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

artículo científico publicado en 2022

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

artículo científico publicado en 2013

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

artículo científico publicado en 2018

Estimating and modeling charge transfer from the SAPT induction energy

artículo científico publicado en 2017

Examining Docking Interactions on ERK2 with Modular Peptide Substrates ⬇️

artículo científico publicado el 18 de octubre de 2011

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

artículo científico publicado en 2012

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

artículo científico publicado el 1 de enero de 2013

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

artículo científico publicado el 6 de agosto de 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2019

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

artículo científico publicado en 2014

Identification and validation of novel PERK inhibitors

artículo científico publicado en 2014

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

artículo científico publicado en 2019

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico publicado el 29 de enero de 2013

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

artículo científico publicado en 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 ⬇️

artículo científico publicado el 2 de enero de 2012

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

artículo científico publicado en 2014

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 ⬇️

artículo científico publicado el 31 de octubre de 2011

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

artículo científico publicado en 2012

Molecular modeling of conformational properties of oligodepsipeptides

artículo científico publicado en 2007

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

artículo científico publicado en 2010

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

artículo científico publicado en 2011

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

artículo científico publicado el 13 de julio de 2010

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

Polarizable molecular dynamics in a polarizable continuum solvent

artículo científico publicado en 2015

Reversible covalent inhibition of eEF-2K by carbonitriles.

artículo científico publicado en 2014

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

Solution NMR insights into docking interactions involving inactive ERK2

artículo científico publicado en 2011

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

artículo científico publicado en 2012

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

artículo científico publicado en 2011

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico publicado en 2013

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

artículo científico publicado en 2012

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

artículo científico publicado en 2016

The molecular mechanism of eukaryotic elongation factor 2 kinase activation

artículo científico publicado en 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

artículo científico publicado en 2021

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 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.

artículo científico publicado en 2014

Lista de obras de 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.