Skip to content

Home Search Authors Pakistan News Saved

SciRah

SciRah does not host or store research papers. Results come live from free, official scholarly APIs, and every paper links back to its original source.

Data sources

OpenAlex
Semantic Scholar
Crossref
CORE
arXiv
PubMed

Privacy policy Terms of service

J. Ponder · SciRah

Researcher profile · Semantic Scholar

J. Ponder

Share profile

J. Ponder — researcher profile on SciRah

h-index: 40
Works: 96
Citations: 13K

Most-cited papers

Force fields for protein simulations.
J. Ponder, D. Case
2003Advances in Protein Chemistry1,697 citations
Semantic Scholar
Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.
J. Ponder, F. Richards
1987Journal of Molecular Biology1,402 citations Open access
Semantic Scholar
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation
Peng-Yu Y. Ren, J. Ponder
20031,329 citations Open access
Semantic Scholar
Current Status of the AMOEBA Polarizable Force Field
J. Ponder, Chuanjie Wu, Peng-Yu Y. Ren, V. Pande +10 more
2010Journal of Physical Chemistry B1,302 citations Open access
Semantic Scholar
An efficient newton‐like method for molecular mechanics energy minimization of large molecules
J. Ponder, Frederic M. Richards
1987739 citations
Semantic Scholar
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins
Yue Shi, Z. Xia, Jia-Jing Zhang, R. Best +3 more
2013Journal of Chemical Theory and Computation632 citations Open access
Semantic Scholar
Tinker 8: Software Tools for Molecular Design
Joshua A. Rackers, Zhi Wang, Chao Lu, Marie L. Laury +5 more
2018Journal of Chemical Theory and Computation623 citations Open access
Semantic Scholar
Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations
Peng-Yu Y. Ren, J. Ponder
2002Journal of Computational Chemistry499 citations
Semantic Scholar
Ion solvation thermodynamics from simulation with a polarizable force field.
Alan Grossfield, Peng-Yu Y. Ren, J. Ponder
2003Journal of the American Chemical Society478 citations
Semantic Scholar
Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules
Peng-Yu Y. Ren, Chuanjie Wu, J. Ponder
2011Journal of Chemical Theory and Computation435 citations Open access
Semantic Scholar
Systematic Improvement of a Classical Molecular Model of Water
Lee-Ping Wang, T. Head-Gordon, J. Ponder, Peng-Yu Y. Ren +4 more
2013Journal of Physical Chemistry B320 citations Open access
Semantic Scholar
AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids
Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu +3 more
2018Journal of Chemical Theory and Computation250 citations Open access
Semantic Scholar
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model
Marie L. Laury, Lee-Ping Wang, V. Pande, T. Head-Gordon +1 more
2015Journal of Physical Chemistry B224 citations Open access
Semantic Scholar
Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization
R. Pappu, Reece K. Hart, J. Ponder
1998217 citations Open access
Semantic Scholar
Temperature and Pressure Dependence of the AMOEBA Water Model
Peng-Yu Y. Ren, J. Ponder
2004198 citations
Semantic Scholar
Accurate modeling of the intramolecular electrostatic energy of proteins
M. Dudek, J. Ponder
1995Journal of Computational Chemistry174 citations Open access
Semantic Scholar
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
Louis Lagardère, Luc-Henri Jolly, Filippo Lipparini, Félix Aviat +11 more
2017Chemical Science155 citations Open access
Semantic Scholar
Light-activated rhodopsin induces structural binding motif in G protein alpha subunit.
O. Kisselev, J. Kao, J. Ponder, Y. Fann +2 more
1998Proceedings of the National Academy of Sciences of the United States of America146 citations Open access
Semantic Scholar
Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization
Craig E. Kundrot, J. Ponder, F. Richards
1991141 citations Open access
Semantic Scholar
Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs
Matthew Harger, Dan Li, Zhi Wang, K. Dalby +4 more
2017Journal of Computational Chemistry104 citations Open access
Semantic Scholar
General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field
Qiantao Wang, Joshua A. Rackers, Chenfeng He, R. Qi +6 more
2015Journal of Chemical Theory and Computation103 citations Open access
Semantic Scholar
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.
C. Hillery, D. J. Mancuso, J. Sadler, J. Ponder +5 more
1998Blood98 citations
Semantic Scholar
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.
M. Schnieders, Nathan A. Baker, Peng-Yu Y. Ren, J. Ponder
2007Journal of Chemical Physics88 citations Open access
Semantic Scholar
Classical Pauli repulsion: An anisotropic, atomic multipole model.
Joshua A. Rackers, J. Ponder
2019Journal of Chemical Physics87 citations Open access
Semantic Scholar
Advanced Potential Energy Surfaces for Molecular Simulation
Alex Albaugh, Henry A. Boateng, Richard T. Bradshaw, Omar N. A. Demerdash +17 more
2016Journal of Physical Chemistry B80 citations Open access
Semantic Scholar
A potential smoothing algorithm accurately predicts transmembrane helix packing
R. Pappu, G. Marshall, J. Ponder
1999Nature Structural Biology79 citations Open access
Semantic Scholar
Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization
Thomas D. Rasmussen, Peng-Yu Y. Ren, J. Ponder, F. Jensen
200774 citations
Semantic Scholar
Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions
M. Dudek, K. Ramnarayan, J. Ponder
1998Journal of Computational Chemistry74 citations
Semantic Scholar
Investigation of Multipole Electrostatics in Hydration Free Energy Calculations
Yue Shi, Chuanjie Wu, J. Ponder, Peng-Yu Y. Ren
2010Journal of Computational Chemistry72 citations Open access
Semantic Scholar
Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems
Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher +8 more
2021Journal of Chemical Theory and Computation69 citations Open access
Semantic Scholar
Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum.
M. Schnieders, J. Ponder
2007Journal of Chemical Theory and Computation68 citations Open access
Semantic Scholar
A Polarizable Water Potential Derived from a Model Electron Density
Joshua A. Rackers, Roseane R. Silva, Zhi Wang, J. Ponder
2021Journal of Chemical Theory and Computation61 citations Open access
Semantic Scholar
TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field.
J. Dziedzic, Yue-Zhi Mao, Yihan Shao, J. Ponder +3 more
2016Journal of Chemical Physics60 citations Open access
Semantic Scholar
An Optimized Charge Penetration Model for Use with the AMOEBA Force Field
Joshua A. Rackers, Qiantao Wang, Cheng-Wen Liu, Jean-Philip Piquemal +2 more
2016Physical Chemistry, Chemical Physics - PCCP59 citations Open access
Semantic Scholar
MSCALE: A General Utility for Multiscale Modeling
H. L. Woodcock, Benjamin T. Miller, M. Hodošček, Asim Okur +3 more
2011Journal of Chemical Theory and Computation52 citations Open access
Semantic Scholar
Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
Félix Aviat, A. Levitt, B. Stamm, Y. Maday +4 more
2016Journal of Chemical Theory and Computation48 citations Open access
Semantic Scholar
Accuracy of side‐chain prediction upon near‐native protein backbones generated by ab initio folding methods
Enoch S. Huang, P. Koehl, M. Levitt, R. Pappu +1 more
1998Proteins: Structure, Function, and Bioinformatics45 citations Open access
Semantic Scholar
Stereochemistry of the hygrolidins
E. J. Corey, J. Ponder
198443 citations
Semantic Scholar
Calculation of the reaction field due to off-center point multipoles
Y. Kong, J. Ponder
199741 citations
Semantic Scholar
Crystal structure of inositol polyphosphate 1-phosphatase at 2.3-A resolution.
J. York, J. Ponder, Zhi-Wei Chen, F. Mathews +1 more
1994Biochemistry41 citations
Semantic Scholar
Calculating binding free energies of host-guest systems using AMOEBA polarizable force field
David R. Bell, R. Qi, Zhifeng Jing, J. Xiang +4 more
2016Physical Chemistry, Chemical Physics - PCCP38 citations Open access
Semantic Scholar
Binding of retinol induces changes in rat cellular retinol-binding protein II conformation and backbone dynamics.
Jian-Yun Lu, Chan-Lan Lin, Chang-Guo Tang, J. Ponder +3 more
2000Journal of Molecular Biology38 citations
Semantic Scholar
The stereochemistry and biosynthesis of hybridalactone, an eicosanoid from
E. J. Corey, B. De, J. Ponder, J. Berg
198434 citations
Semantic Scholar
Absolute Binding Free Energies for the SAMPL6 Cucurbit[8]uril Host-Guest Challenge via the AMOEBA Polarizable Force Field
Marie L. Laury, Zhi Wang, Aaron S. Gordon, J. Ponder
2018Journal of Computer-Aided Molecular Design33 citations Open access
Semantic Scholar
The structure and dynamics of rat apo-cellular retinol-binding protein II in solution: comparison with the X-ray structure.
Jian-Yun Lu, Chan-Lan Lin, Chang-Guo Tang, J. Ponder +3 more
1999Journal of Molecular Biology33 citations
Semantic Scholar
An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field
J. Xiang, J. Ponder
2013Journal of Chemical Theory and Computation32 citations Open access
Semantic Scholar
Synthesis of a stable analog of thromboxane A2 with methylene replacing the 9,11-bridging oxygen
E. J. Corey, J. Ponder, P. Ulrich
198031 citations
Semantic Scholar
An empirical extrapolation scheme for efficient treatment of induced dipoles.
Andrew C. Simmonett, Frank C. Pickard, J. Ponder, B. Brooks
2016Journal of Chemical Physics30 citations Open access
Semantic Scholar
A Polarizable Multipole-based Force Field for Dimethyl and Trimethyl Phosphate
Changsheng Zhang, Chao Lu, Qiantao Wang, J. Ponder +1 more
2015Journal of Chemical Theory and Computation29 citations Open access
Semantic Scholar
A Valence Bond Model for Aqueous Cu(II) and Zn(II) Ions in the AMOEBA Polarizable Force Field
J. Xiang, J. Ponder
2012Journal of Computational Chemistry29 citations Open access
Semantic Scholar

Frequent co-authors

Invite them to SciRah by sharing their profile.

Peng-Yu Y. Ren×21
Invite
Peng-Yu Y. Ren — researcher profile on SciRah
Jean-Philip Piquemal×8
Invite
Jean-Philip Piquemal — researcher profile on SciRah
M. Schnieders×6
Invite
M. Schnieders — researcher profile on SciRah
Louis Lagardère×6
Invite
Louis Lagardère — researcher profile on SciRah

×5

Invite

Chuanjie Wu — researcher profile on SciRah

T. Head-Gordon×5

Invite

T. Head-Gordon — researcher profile on SciRah

Joshua A. Rackers×5

Invite

Joshua A. Rackers — researcher profile on SciRah

Invite

Zhi Wang — researcher profile on SciRah

Invite

V. Pande — researcher profile on SciRah

M. Head-Gordon×3

Invite

M. Head-Gordon — researcher profile on SciRah

Invite

Chao Lu — researcher profile on SciRah

Marie L. Laury×3

Invite

Marie L. Laury — researcher profile on SciRah