Pengyu Ren

发表

The head fixation based on skull cap: An improved protocol used in single unit recording in the vestibular system

Qing Zhang, Peng Han, Pengyu Ren, 2020, MethodsX.

Faculty Opinions recommendation of Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size.

Pengyu Ren, Chengwen Liu, 2018 .

Faculty Opinions recommendation of General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins.

Pengyu Ren, Chengwen Liu, 2019 .

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0] pdf

Jean-Philip Piquemal, Alejandro Duran, Louis Lagardère, 2019, ArXiv.

Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]

Jean-Philip Piquemal, Alejandro Duran, Jay W. Ponder, 2019, Living Journal of Computational Molecular Science.

Estimating and modeling charge transfer from the SAPT induction energy

Qiantao Wang, Shi Deng, Pengyu Ren, 2017, J. Comput. Chem..

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

Jean-Philip Piquemal, Zhi Wang, Jay W. Ponder, 2020, ArXiv.

Faculty Opinions recommendation of A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning.

Pengyu Ren, Chengwen Liu, 2019 .

Tinker 8: Software Tools for Molecular Design.

Jean-Philip Piquemal, Zhi Wang, Louis Lagardère, 2018, Journal of chemical theory and computation.

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations

Benjamin Stamm, Yvon Maday, Jean-Philip Piquemal, 2014 .

A Simple Crowdfunding Model

Pengyu Ren, 2017 .

Systematic Improvement on the Classical Molecular Model of Water

Vijay S. Pande, John D. Chodera, Jay W. Ponder, 2014 .

Virtual Reality Training with Passive Haptic Feedback for CryoEM Sample Preparation

Cheryl Z. Qian, Victor Y. Chen, Jun Zhang, 2019, 2019 IEEE Conference on Virtual Reality and 3D User Interfaces (VR).

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

Ray Luo, Changhao Wang, Pengyu Ren, 2016, J. Comput. Chem..

Imaging sub-diffuse optical properties of cancerous and normal skin tissue using machine learning-aided spatial frequency domain imaging

Mia K. Markey, Xu Feng, James W. Tunnell, 2021, Journal of biomedical optics.

Polarizable molecular dynamics in a polarizable continuum solvent.

Benjamin Stamm, Yvon Maday, Jean-Philip Piquemal, 2015, Journal of chemical theory and computation.

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

Pengyu Ren, Kevin N Dalby, Pengyu Y. Ren, 2012, ACS medicinal chemistry letters.

Computational and Experimental Studies of Inhibitor Design for Aldolase A.

Pengyu Ren, Zhifeng Jing, Kevin N Dalby, 2019, The journal of physical chemistry. B.

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

Jean-Philip Piquemal, Kevin N. Dalby, Stephen D. Fried, 2014, The journal of physical chemistry. B.

Polarizable Force Fields for Scoring Protein–Ligand Interactions

Jiajing Zhang, Pengyu Ren, Pengyu Y. Ren, 2012 .

Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

Nohad Gresh, Jean-Philip Piquemal, Pengyu Ren, 2012, Theoretical Chemistry Accounts.

AMOEBA+ Classical Potential for Modeling Molecular Interactions.

Jean-Philip Piquemal, Pengyu Ren, Chengwen Liu, 2019, Journal of chemical theory and computation.

RNA 3D structure prediction by using a coarse-grained model and experimental data.

Pengyu Ren, Pengyu Y. Ren, David R. Bell, 2013, The journal of physical chemistry. B.

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

Yan Li, Pengyu Ren, Guohui Li, 2014, Journal of chemical theory and computation.

Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.

Jean-Philip Piquemal, Pengyu Ren, Robin Chaudret, 2010, Journal of Chemical Theory and Computation.

Many-Body Effects and Electrostatics in Biomolecules

Markus Meuwly, Pengyu Ren, Qiang Cui, 2016 .

Trypsin-ligand binding free energy calculation with AMOEBA

Dian Jiao, Pengyu Ren, Michael J. Schnieders, 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Prediction and Coarse-Grained Modeling of RNA Structures

Pengyu Ren, Pengyu Y. Ren, Z. Xia, 2013 .

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

Benjamin Stamm, Yvon Maday, Jean-Philip Piquemal, 2016, Journal of chemical theory and computation.

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.

Nathan A. Baker, Jay W Ponder, Nathan A Baker, 2007, The Journal of chemical physics.

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

Alan Grossfield, Dian Jiao, Pengyu Ren, 2006, The journal of physical chemistry. B.

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

Peter D. Crompton, Pengyu Ren, Pengyu Y. Ren, 2017, Nature Communications.

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

Jay W Ponder, Pengyu Ren, Michael J Schnieders, 2016, Physical chemistry chemical physics : PCCP.

A physically grounded damped dispersion model with particle mesh Ewald summation.

Jay W Ponder, Chengwen Liu, Pengyu Ren, 2018, The Journal of chemical physics.

Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases

Matthew Harger, Pengyu Ren, Pengyu Y. Ren, 2016, Journal of chemical theory and computation.

Accurate Immune Repertoire Sequencing Reveals Malaria Infection Driven Antibody Lineage Diversification in Young Children

Peter D. Crompton, Pengyu Ren, Ning Jiang, 2017 .

Automation of AMOEBA polarizable force field parameterization for small molecules

Pengyu Ren, Pengyu Y. Ren, Johnny C. Wu, 2012, Theoretical Chemistry Accounts.

Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization

Frank Jensen, Jay W. Ponder, Pengyu Ren, 2007 .

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

Wei Yang, Jonas Baltrusaitis, Lianqing Zheng, 2012, Journal of chemical theory and computation.

Molecular docking simulations for macromolecularly imprinted polymers.

Nicholas A Peppas, Pengyu Ren, David R Kryscio, 2011, Industrial & engineering chemistry research.

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

Wei Yang, Jayvee R. Abella, Pengyu Ren, 2014, Journal of chemical theory and computation.

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

Jean-Philip Piquemal, Jay W. Ponder, Pengyu Ren, 2018, Journal of chemical theory and computation.

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

Nohad Gresh, Jean-Philip Piquemal, Jay W. Ponder, 2015, Journal of chemical theory and computation.

Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations.

Pengyu Ren, Pengyu Y. Ren, Yue Shi, 2012, The journal of physical chemistry. B.

Biomolecular electrostatics and solvation: a computational perspective

Nathan A. Baker, Jaehun Chun, Jiajing Zhang, 2012, Quarterly Reviews of Biophysics.

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

Wei Yang, Jean-Philip Piquemal, Jiajing Zhang, 2012, Journal of chemical theory and computation.

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

Benjamin Stamm, Yvon Maday, Jean-Philip Piquemal, 2014, Journal of chemical theory and computation.

Virtual screening using molecular simulations

Ray Luo, Tianyi Yang, Pengyu Ren, 2011, Proteins.

A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics

Pengyu Ren, Guohui Li, Pengyu Y. Ren, 2012 .

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

Laura J Suggs, Pengyu Ren, Pengyu Y. Ren, 2012, Biomacromolecules.

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

James W Tunnell, Pengyu Ren, Pengyu Y. Ren, 2010, Journal of molecular graphics & modelling.