J. Ponder

发表

Accuracy of side‐chain prediction upon near‐native protein backbones generated by ab initio folding methods

M. Levitt, P. Koehl, E. Huang, 1998, Proteins.

An efficient newton‐like method for molecular mechanics energy minimization of large molecules

J. Ponder, F. Richards, 1987 .

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.

J. Ponder, F. Richards, 1987, Journal of molecular biology.

Force fields for protein simulations.

J. Ponder, D. Case, 2003, Advances in protein chemistry.

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Pengyu Y. Ren, J. Ponder, 2003 .

Systematic improvement of a classical molecular model of water.

Pengyu Y. Ren, J. Ponder, V. Pande, 2013, The journal of physical chemistry. B.

Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions.

E. Huang, J. Ponder, R. Samudrala, 1999, Journal of molecular biology.

Calculation of the reaction field due to off-center point multipoles

J. Ponder, Y. Kong, 1997 .

Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

J. Ponder, K. Ramnarayan, M. Dudek, 1998 .

Crystal structure of inositol polyphosphate 1-phosphatase at 2.3-A resolution.

F. S. Mathews, J. Ponder, J. York, 1994, Biochemistry.

Type 2M von Willebrand disease: F606I and I662F mutations in the glycoprotein Ib binding domain selectively impair ristocetin- but not botrocetin-mediated binding of von Willebrand factor to platelets.

J. Ponder, R. Montgomery, J. Gill, 1998, Blood.

The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm.

J. Ponder, M. Hodsdon, D. Cistola, 1996, Journal of molecular biology.

Current status of the AMOEBA polarizable force field.

Margaret E. Johnson, Pengyu Y. Ren, J. Ponder, 2010, The journal of physical chemistry. B.

Ion solvation thermodynamics from simulation with a polarizable force field.

Pengyu Y. Ren, J. Ponder, A. Grossfield, 2003, Journal of the American Chemical Society.

Temperature and Pressure Dependence of the AMOEBA Water Model

Pengyu Y. Ren, J. Ponder, 2004 .

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

Pengyu Y. Ren, J. Ponder, Chuanjie Wu, 2011, Journal of chemical theory and computation.

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

Pengyu Y. Ren, J. Ponder, R. Best, 2013, Journal of chemical theory and computation.

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

Joshua A. Rackers, Pengyu Y. Ren, J. Ponder, 2016, Physical chemistry chemical physics : PCCP.

Electrostatics in the AMOEBA force field: The long and the short of it

J. Ponder, 2013 .

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Jay W Ponder, Vijay S Pande, Teresa Head-Gordon, 2015, The journal of physical chemistry. B.

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.

Exploring the similarities between potential smoothing and simulated annealing

Jay W. Ponder, Rohit V. Pappu, Reece K. Hart, 2000 .

A potential smoothing algorithm accurately predicts transmembrane helix packing

Garland R. Marshall, Jay W. Ponder, Rohit V. Pappu, 1999, Nature Structural Biology.

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.

Definition of a metal-dependent/Li(+)-inhibited phosphomonoesterase protein family based upon a conserved three-dimensional core structure.

J. Ponder, J. York, P. Majerus, 1995, Proceedings of the National Academy of Sciences of the United States of America.

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.

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.

Brandon D. Walker, Pengyu Y. Ren, J. Ponder, 2020, Journal of chemical theory and computation.

Synthesis of a stable analog of thromboxane A2 with methylene replacing the 9,11-bridging oxygen

J. Ponder, E. Corey, P. Ulrich, 1980 .

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate

Pengyu Y. Ren, J. Ponder, Changsheng Zhang, 2015, Journal of chemical theory and computation.

Helix stability of oligoglycine, oligoalanine, and oligo‐β‐alanine dodecamers reflected by hydrogen‐bond persistence

Jay W Ponder, Garland R Marshall, J. Ponder, 2014, Proteins.

Stereochemistry of the hygrolidins

Jay W. Ponder, J. Ponder, E. Corey, 1984 .

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

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

Accurate modeling of the intramolecular electrostatic energy of proteins

Jay W. Ponder, Michael J. Dudek, J. Ponder, 1995, J. Comput. Chem..

Synthesis of 4-methyl-3-heptanol and 4-methyl-3-heptanone. Two easily synthesized insect pheromones

R. S. Lenox, J. Ponder, R. Einterz, 1977 .

Binding of retinol induces changes in rat cellular retinol-binding protein II conformation and backbone dynamics.

J. Ponder, D. Cistola, J. Lu, 2000, Journal of molecular biology.

The stereochemistry and biosynthesis of hybridalactone, an eicosanoid from

J. Berg, J. Ponder, E. Corey, 1984 .

SYNTHESIS OF A STABLE ANALOG OF THROMBOXANE A2 WITH METHYLENE REPLACING THE 9,11 BRIDGING OXYGEN

J. Ponder, E. Corey, P. Ulrich, 1980 .

Type 2M von Willebrand Disease: F606I and I662F Mutations in the Glycoprotein Ib Binding Domain Selectively Impair Ristocetin- but not Botrocetin-Mediated Binding of von Willebrand Factor to Platelets

J. Ponder, J. Scott, R. Montgomery, 1998 .

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04531j

Nohad Gresh, Benjamin Stamm, Yvon Maday, 2017, Chemical science.

Tinker 8: Software Tools for Molecular Design.

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

Tertiary Templates for Proteins Use of Packing Criteria in the Enumeration of Allowed Different Structural Classes Sequences

Jay W. Ponder, Frederic M. Richards, J. Ponder, 1987 .

Crystallization and initial X-ray crystallographic characterization of recombinant bovine inositol polyphosphate 1-phosphatase produced in Spodoptera frugiperda cells.

J. Ponder, J. York, Z. Chen, 1994, Journal of molecular biology.

The structure and dynamics of rat apo-cellular retinol-binding protein II in solution: comparison with the X-ray structure.

J. Ponder, D. Cistola, J. Lu, 1999, Journal of molecular biology.

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

Daniel J. Kuster, J. Ponder, G. Marshall, 2015, PloS one.

Internal packing and protein structural classes.

F M Richards, J. Ponder, F. Richards, 1987, Cold Spring Harbor symposia on quantitative biology.

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

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

Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations

Pengyu Y. Ren, Jay W. Ponder, Pengyu Y. Ren, 2002, J. Comput. Chem..

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field.

Jay W Ponder, Jin Yu Xiang, J. Ponder, 2014, Journal of chemical theory and computation.

Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization

Jay W. Ponder, Rohit V. Pappu, Reece K. Hart, 1998 .

Classical Exchange Polarization: An Anisotropic Variable Polarizability Model.

Joshua A. Rackers, J. Ponder, Zhi Wang, 2022, The journal of physical chemistry. B.

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.

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

Jay W. Ponder, Jin Yu Xiang, J. Ponder, 2013, J. Comput. Chem..

Light-activated rhodopsin induces structural binding motif in G protein alpha subunit.

G R Marshall, J. Ponder, G. Marshall, 1998, Proceedings of the National Academy of Sciences of the United States of America.

MSCALE: A General Utility for Multiscale Modeling.

Asim Okur, Bernard R Brooks, Benjamin T. Miller, 2011, Journal of chemical theory and computation.

AMOEBA binding free energies for the SAMPL7 TrimerTrip host–guest challenge

Marie L. Laury, J. Ponder, Yuanjun Shi, 2020, Journal of Computer-Aided Molecular Design.

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

Zhi Wang, Jean-Philip Piquemal, Kevin N. Dalby, 2017, J. Comput. Chem..

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

Nohad Gresh, Jean-Philip Piquemal, Qiantao Wang, 2016, J. Comput. Chem..

Advanced Potential Energy Surfaces for Molecular Simulation.

Jonathan W Essex, Qiao Zeng, Jay W Ponder, 2016, The journal of physical chemistry. B.

Classical Pauli repulsion: An anisotropic, atomic multipole model.

Jay W Ponder, Joshua A. Rackers, J. Ponder, 2019, The Journal of chemical physics.

Absolute binding free energies for the SAMPL6 cucurbit[8]uril host–guest challenge via the AMOEBA polarizable force field

Zhi Wang, Jay W. Ponder, Marie L. Laury, 2018, Journal of Computer-Aided Molecular Design.

A structural basis for lithium and substrate binding of an inositide phosphatase

J. Ponder, J. York, J. Xiong, 2020, The Journal of biological chemistry.

Computationally driven discovery of SARS-CoV-2 Mpro inhibitors: from design to experimental validation

Pengyu Y. Ren, J. Ponder, M. Sturlese, 2021, Chemical science.

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field.

Yihan Shao, Chris-Kriton Skylaris, Jacek Dziedzic, 2016, The Journal of chemical physics.

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.

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

Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum.

Jay W Ponder, Michael J Schnieders, J. Ponder, 2007, Journal of chemical theory and computation.

Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization

Jay W. Ponder, Craig E. Kundrot, Frederic M. Richards, 1991 .

A Polarizable Water Potential Derived from a Model Electron Density

Joshua A. Rackers, Roseane R Silva, J. Ponder, 2021, 2106.13116.

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

Pengyu Y. Ren, J. Ponder, J. Piquemal, 2021, Journal of chemical theory and computation.

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.

An empirical extrapolation scheme for efficient treatment of induced dipoles.

Andrew C Simmonett, Bernard R Brooks, Jay W Ponder, 2016, The Journal of chemical physics.

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.

Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field

J. Ponder, Borna Novak, Ryan J. Miller, 2023, J. Chem. Inf. Model..

Multipole electrostatics in hydration free energy calculations

Yue Shi, Pengyu Y. Ren, Jay W. Ponder, 2011, J. Comput. Chem..

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

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

Molecular dynamics of β-hairpin models of epigenetic recognition motifs.

J. Ponder, G. Marshall, Chuanjie Wu, 2012, Journal of the American Chemical Society.

Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

Jay W. Ponder, Michael J. Dudek, K. Ramnarayan, 1998, J. Comput. Chem..

Turn scanning. Experimental and theoretical approaches to the role of turns.

E. Huang, J. Ponder, Carl Frieden, 2001, Methods in molecular biology.

Exploring the similarities between potential smoothing and simulated annealing

Jay W. Ponder, Rohit V. Pappu, Reece K. Hart, 2000, J. Comput. Chem..

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

Pengyu Y. Ren, J. Ponder, F. Lipparini, 2017, Chemical science.

A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model.

Pengyu Y. Ren, J. Ponder, T. Casavant, 2023, The Journal of chemical physics.

Tinker 8: Software Tools for Molecular Design.

Marie L. Laury, Joshua A. Rackers, Pengyu Y. Ren, 2018, Journal of chemical theory and computation.

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

Pengyu Y. Ren, J. Ponder, Matthew Harger, 2017, J. Comput. Chem..

Polarizable Water Potential Derived from a Model Electron Density.

Joshua A. Rackers, Roseane R Silva, J. Ponder, 2021, Journal of chemical theory and computation.

Classical Pauli repulsion: An anisotropic, atomic multipole model.

Joshua A. Rackers, J. Ponder, 2019, The Journal of chemical physics.

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pKa corrections

Bernard R. Brooks, Juyong Lee, Gerhard König, 2016, Journal of Computer-Aided Molecular Design.