| Year |
Citation |
Score |
| 2024 |
Bone RA, Chung MKJ, Ponder JW, Riccardi D, Muzny C, Sundararaman R, Schwarz K. A new method to calculate broadband dielectric spectra of solvents from molecular dynamics simulations demonstrated with polarizable force fields. The Journal of Chemical Physics. 161. PMID 39132799 DOI: 10.1063/5.0217883 |
0.407 |
|
| 2024 |
Gogal RA, Nessler AJ, Thiel AC, Bernabe HV, Corrigan Grove RA, Cousineau LM, Litman JM, Miller JM, Qi G, Speranza MJ, Tollefson MR, Fenn TD, Michaelson JJ, Okada O, Piquemal JP, ... Ponder JW, et al. Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. The Journal of Chemical Physics. 161. PMID 38958156 DOI: 10.1063/5.0214652 |
0.559 |
|
| 2024 |
Chung MKJ, Ponder JW. Beyond isotropic repulsion: Classical anisotropic repulsion by inclusion of p orbitals. The Journal of Chemical Physics. 160. PMID 38748037 DOI: 10.1063/5.0203678 |
0.363 |
|
| 2024 |
Thiel AC, Speranza MJ, Jadhav S, Stevens LL, Unruh DK, Ren P, Ponder JW, Shen J, Schnieders MJ. Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation. PMID 38507252 DOI: 10.1021/acs.jctc.3c01180 |
0.756 |
|
| 2023 |
Corrigan RA, Thiel AC, Lynn JR, Casavant TL, Ren P, Ponder JW, Schnieders MJ. A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. The Journal of Chemical Physics. 159. PMID 37526158 DOI: 10.1063/5.0158914 |
0.758 |
|
| 2023 |
Chung MKJ, Miller RJ, Novak B, Wang Z, Ponder JW. Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. Journal of Chemical Information and Modeling. PMID 37075788 DOI: 10.1021/acs.jcim.3c00155 |
0.436 |
|
| 2022 |
Chung MKJ, Wang Z, Rackers JA, Ponder JW. Classical Exchange Polarization: An Anisotropic Variable Polarizability Model. The Journal of Physical Chemistry. B. PMID 36166814 DOI: 10.1021/acs.jpcb.2c04237 |
0.328 |
|
| 2022 |
El Khoury L, Jing Z, Cuzzolin A, Deplano A, Loco D, Sattarov B, Hédin F, Wendeborn S, Ho C, El Ahdab D, Jaffrelot Inizan T, Sturlese M, Sosic A, Volpiana M, Lugato A, ... ... Ponder JW, et al. Computationally driven discovery of SARS-CoV-2 M inhibitors: from design to experimental validation. Chemical Science. 13: 3674-3687. PMID 35432906 DOI: 10.1039/d1sc05892d |
0.646 |
|
| 2021 |
Rackers JA, Silva RR, Wang Z, Ponder JW. Polarizable Water Potential Derived from a Model Electron Density. Journal of Chemical Theory and Computation. 17: 7056-7084. PMID 34699197 DOI: 10.1021/acs.jctc.1c00628 |
0.363 |
|
| 2021 |
Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation. PMID 33769814 DOI: 10.1021/acs.jctc.0c01286 |
0.803 |
|
| 2021 |
Adjoua O, Lagardère L, Jolly LH, Durocher A, Very T, Dupays I, Wang Z, Inizan TJ, Célerse F, Ren P, Ponder JW, Piquemal JP. Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems. Journal of Chemical Theory and Computation. PMID 33755446 DOI: 10.1021/acs.jctc.0c01164 |
0.583 |
|
| 2020 |
Adjoua O, Lagardère L, Jolly LH, Durocher A, Very T, Dupays I, Wang Z, Inizan TJ, Célerse F, Ren P, Ponder JW, Piquemal JP. Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. Arxiv. PMID 33173801 |
0.579 |
|
| 2020 |
Shi Y, Laury ML, Wang Z, Ponder JW. AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge. Journal of Computer-Aided Molecular Design. PMID 33140208 DOI: 10.1007/s10822-020-00358-2 |
0.346 |
|
| 2019 |
Rackers JA, Ponder JW. Classical Pauli repulsion: An anisotropic, atomic multipole model. The Journal of Chemical Physics. 150: 084104. PMID 30823770 DOI: 10.1063/1.5081060 |
0.488 |
|
| 2019 |
Jolly L, Duran A, Lagardère L, Ponder JW, Ren P, Piquemal J. Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0] Living Journal of Computational Molecular Science. 1. DOI: 10.33011/Livecoms.1.2.10409 |
0.564 |
|
| 2018 |
Laury ML, Wang Z, Gordon AS, Ponder JW. Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field. Journal of Computer-Aided Molecular Design. PMID 30324303 DOI: 10.1007/S10822-018-0147-5 |
0.428 |
|
| 2018 |
Rackers JA, Liu C, Ren P, Ponder JW. A physically grounded damped dispersion model with particle mesh Ewald summation. The Journal of Chemical Physics. 149: 084115. PMID 30193468 DOI: 10.1063/1.5030434 |
0.644 |
|
| 2018 |
Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. Journal of Chemical Theory and Computation. 14: 5273-5289. PMID 30176213 DOI: 10.1021/Acs.Jctc.8B00529 |
0.752 |
|
| 2018 |
Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chemical Science. 9: 956-972. PMID 29732110 DOI: 10.1039/C7Sc04531J |
0.783 |
|
| 2018 |
Zhang C, Lu C, Jing Z, Wu C, Piquemal JP, Ponder JW, Ren P. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. Journal of Chemical Theory and Computation. PMID 29438622 DOI: 10.1021/Acs.Jctc.7B01169 |
0.673 |
|
| 2017 |
Harger M, Li D, Wang Z, Dalby K, Lagardère L, Piquemal JP, Ponder J, Ren P. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. Journal of Computational Chemistry. 38: 2047-2055. PMID 28600826 DOI: 10.1002/Jcc.24853 |
0.6 |
|
| 2017 |
Aviat F, Levitt A, Stamm B, Maday Y, Ren P, Ponder JW, Lagardère L, Piquemal JP. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations. Journal of Chemical Theory and Computation. 13: 180-190. PMID 28068773 DOI: 10.1021/Acs.Jctc.6B00981 |
0.565 |
|
| 2016 |
Rackers JA, Wang Q, Liu C, Piquemal JP, Ren P, Ponder JW. An optimized charge penetration model for use with the AMOEBA force field. Physical Chemistry Chemical Physics : Pccp. PMID 27901142 DOI: 10.1039/C6Cp06017J |
0.694 |
|
| 2016 |
Simmonett AC, Pickard FC, Ponder JW, Brooks BR. An empirical extrapolation scheme for efficient treatment of induced dipoles. The Journal of Chemical Physics. 145: 164101. PMID 27802661 DOI: 10.1063/1.4964866 |
0.34 |
|
| 2016 |
Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. The Journal of Chemical Physics. 145: 124106. PMID 27782640 DOI: 10.1063/1.4962909 |
0.459 |
|
| 2016 |
Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails JM, Zeng Q, Case DA, Eastman PK, Essex JW, Head-Gordon M, Pande VS, Ponder JW, et al. Advanced Potential Energy Surfaces for Molecular Simulation. The Journal of Physical Chemistry. B. PMID 27513316 DOI: 10.1021/Acs.Jpcb.6B06414 |
0.495 |
|
| 2016 |
Bell DR, Qi R, Jing Z, Xiang JY, Mejias C, Schnieders MJ, Ponder JW, Ren P. Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field. Physical Chemistry Chemical Physics : Pccp. PMID 27254477 DOI: 10.1039/C6Cp02509A |
0.773 |
|
| 2016 |
Narth C, Lagardère L, Polack É, Gresh N, Wang Q, Bell DR, Rackers JA, Ponder JW, Ren PY, Piquemal JP. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. Journal of Computational Chemistry. 37: 494-506. PMID 26814845 DOI: 10.1002/Jcc.24257 |
0.608 |
|
| 2016 |
Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field Journal of Chemical Physics. 145. DOI: 10.1063/1.4962909 |
0.356 |
|
| 2015 |
Zhang C, Lu C, Wang Q, Ponder JW, Ren P. Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate. Journal of Chemical Theory and Computation. 11: 5326-39. PMID 26574325 DOI: 10.1021/Acs.Jctc.5B00562 |
0.666 |
|
| 2015 |
Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field. Journal of Chemical Theory and Computation. 11: 2609-2618. PMID 26413036 DOI: 10.1021/Acs.Jctc.5B00267 |
0.658 |
|
| 2015 |
Kuster DJ, Liu C, Fang Z, Ponder JW, Marshall GR. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics. Plos One. 10: e0123146. PMID 25894612 DOI: 10.1371/Journal.Pone.0123146 |
0.389 |
|
| 2015 |
Laury ML, Wang LP, Pande VS, Head-Gordon T, Ponder JW. Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. The Journal of Physical Chemistry. B. 119: 9423-37. PMID 25683601 DOI: 10.1021/Jp510896N |
0.392 |
|
| 2015 |
Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field Journal of Chemical Theory and Computation. 11: 2609-2618. DOI: 10.1021/acs.jctc.5b00267 |
0.576 |
|
| 2014 |
Xiang JY, Ponder JW. An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field. Journal of Chemical Theory and Computation. 10: 298-311. PMID 25045338 DOI: 10.1021/Ct400778H |
0.417 |
|
| 2014 |
Wang L, Head-Gordon T, Ponder J, Ren P, Chodera J, Eastman P, Martinez TJ, Pande VS. Systematic Improvement on the Classical Molecular Model of Water Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2273 |
0.563 |
|
| 2013 |
Shi Y, Xia Z, Zhang J, Best R, Wu C, Ponder JW, Ren P. The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation. 9: 4046-4063. PMID 24163642 DOI: 10.1021/Ct4003702 |
0.678 |
|
| 2013 |
Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS. Systematic improvement of a classical molecular model of water. The Journal of Physical Chemistry. B. 117: 9956-72. PMID 23750713 DOI: 10.1021/Jp403802C |
0.57 |
|
| 2013 |
Xiang JY, Ponder JW. A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field. Journal of Computational Chemistry. 34: 739-49. PMID 23212979 DOI: 10.1002/Jcc.23190 |
0.429 |
|
| 2012 |
Zheng X, Wu C, Ponder JW, Marshall GR. Molecular dynamics of β-hairpin models of epigenetic recognition motifs. Journal of the American Chemical Society. 134: 15970-8. PMID 22934656 DOI: 10.1021/Ja306803V |
0.386 |
|
| 2011 |
Ren P, Wu C, Ponder JW. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. Journal of Chemical Theory and Computation. 7: 3143-3161. PMID 22022236 DOI: 10.1021/Ct200304D |
0.633 |
|
| 2011 |
Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW, Brooks BR. MSCALE: A General Utility for Multiscale Modeling. Journal of Chemical Theory and Computation. 7: 1208-1219. PMID 21691425 DOI: 10.1021/Ct100738H |
0.471 |
|
| 2011 |
Shi Y, Wu C, Ponder JW, Ren P. Multipole electrostatics in hydration free energy calculations. Journal of Computational Chemistry. 32: 967-77. PMID 20925089 DOI: 10.1002/Jcc.21681 |
0.654 |
|
| 2010 |
Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/Jp910674D |
0.79 |
|
| 2009 |
Kuster DJ, Urahata S, Ponder JW, Marshall GR. From Data or Dogma? The Myth of the Ideal Helix Biophysical Journal. 96: 5a. DOI: 10.1016/J.Bpj.2008.12.918 |
0.414 |
|
| 2007 |
Schnieders MJ, Ponder JW. Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum. Journal of Chemical Theory and Computation. 3: 2083-97. PMID 26636202 DOI: 10.1021/Ct7001336 |
0.75 |
|
| 2007 |
Schnieders MJ, Baker NA, Ren P, Ponder JW. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. The Journal of Chemical Physics. 126: 124114. PMID 17411115 DOI: 10.1063/1.2714528 |
0.78 |
|
| 2007 |
Rasmussen TD, Ren P, Ponder JW, Jensen F. Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization International Journal of Quantum Chemistry. 107: 1390-1395. DOI: 10.1002/Qua.21278 |
0.629 |
|
| 2004 |
Ren P, Ponder JW. Temperature and pressure dependence of the AMOEBA water model Journal of Physical Chemistry B. 108: 13427-13437. DOI: 10.1021/Jp0484332 |
0.515 |
|
| 2003 |
Grossfield A, Ren P, Ponder JW. Ion solvation thermodynamics from simulation with a polarizable force field. Journal of the American Chemical Society. 125: 15671-82. PMID 14664617 DOI: 10.1021/Ja037005R |
0.731 |
|
| 2003 |
Ponder JW, Case DA. Force fields for protein simulations. Advances in Protein Chemistry. 66: 27-85. PMID 14631816 DOI: 10.1016/S0065-3233(03)66002-X |
0.516 |
|
| 2003 |
Ren P, Ponder JW. Polarizable atomic multipole water model for molecular mechanics simulation Journal of Physical Chemistry B. 107: 5933-5947. DOI: 10.1021/Jp027815+ |
0.593 |
|
| 2002 |
Ren P, Ponder JW. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. Journal of Computational Chemistry. 23: 1497-506. PMID 12395419 DOI: 10.1002/Jcc.10127 |
0.613 |
|
| 2000 |
Lu J, Lin CL, Tang C, Ponder JW, Kao JLF, Cistola DP, Li E. Binding of retinol induces changes in rat cellular retinol-binding protein II conformation and backbone dynamics Journal of Molecular Biology. 300: 619-632. PMID 10884357 DOI: 10.1006/Jmbi.2000.3883 |
0.34 |
|
| 2000 |
Hart RK, Pappu RV, Ponder JW. Exploring the Similarities between Potential Smoothing and Simulated Annealing Journal of Computational Chemistry. 21: 531-552. DOI: 10.1002/(Sici)1096-987X(200005)21:7<531::Aid-Jcc3>3.0.Co;2-C |
0.6 |
|
| 1999 |
Huang ES, Samudrala R, Ponder JW. Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. Journal of Molecular Biology. 290: 267-81. PMID 10388572 DOI: 10.1006/Jmbi.1999.2861 |
0.366 |
|
| 1999 |
Lu J, Lin CL, Tang C, Ponder JW, Kao JLF, Cistola DP, Li E. The structure and dynamics of rat apo-cellular retinol-binding protein II in solution: Comparison with the X-ray structure Journal of Molecular Biology. 286: 1179-1195. PMID 10047490 DOI: 10.1006/Jmbi.1999.2544 |
0.338 |
|
| 1999 |
Pappu RV, Marshall GR, Ponder JW. A potential smoothing algorithm accurately predicts transmembrane helix packing. Nature Structural Biology. 6: 50-5. PMID 9886292 DOI: 10.1038/4922 |
0.59 |
|
| 1998 |
Huang ES, Koehl P, Levitt M, Pappu RV, Ponder JW. Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods. Proteins. 33: 204-17. PMID 9779788 DOI: 10.1002/(Sici)1097-0134(19981101)33:2<204::Aid-Prot5>3.0.Co;2-I |
0.56 |
|
| 1998 |
Huang ES, Samudrala R, Ponder JW. Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures. Protein Science : a Publication of the Protein Society. 7: 1998-2003. PMID 9761481 DOI: 10.1002/Pro.5560070916 |
0.369 |
|
| 1998 |
Pappu RV, Hart RK, Ponder JW. Analysis and application of potential energy smoothing and search methods for global optimization Journal of Physical Chemistry B. 102: 9725-9742. DOI: 10.1021/Jp982255T |
0.578 |
|
| 1998 |
Dudek MJ, Ramnarayan K, Ponder JW. Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions Journal of Computational Chemistry. 19: 548-573. DOI: 10.1002/(Sici)1096-987X(19980415)19:5<548::Aid-Jcc7>3.0.Co;2-M |
0.41 |
|
| 1997 |
Kong Y, Ponder JW. Calculation of the reaction field due to off-center point multipoles The Journal of Chemical Physics. 107: 481-492. DOI: 10.1063/1.474409 |
0.452 |
|
| 1996 |
Hodsdon ME, Ponder JW, Cistola DP. The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: Application of a novel distance geometry algorithm Journal of Molecular Biology. 264: 585-602. PMID 8969307 DOI: 10.1006/Jmbi.1996.0663 |
0.355 |
|
| 1995 |
Dudek MJ, Ponder JW. Accurate modeling of the intramolecular electrostatic energy of proteins Journal of Computational Chemistry. 16: 791-816. DOI: 10.1002/Jcc.540160702 |
0.466 |
|
| 1991 |
Kundrot CE, Ponder JW, Richards FM. Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization Journal of Computational Chemistry. 12: 402-409. DOI: 10.1002/Jcc.540120314 |
0.387 |
|
| 1987 |
Ponder JW, Richards FM. Internal packing and protein structural classes. Cold Spring Harbor Symposia On Quantitative Biology. 52: 421-8. PMID 2841069 DOI: 10.1101/Sqb.1987.052.01.049 |
0.345 |
|
| 1987 |
Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. Journal of Molecular Biology. 193: 775-91. PMID 2441069 DOI: 10.1016/0022-2836(87)90358-5 |
0.352 |
|
| 1987 |
Ponder JW, Richards FM. An efficient newton-like method for molecular mechanics energy minimization of large molecules Journal of Computational Chemistry. 8: 1016-1024. DOI: 10.1002/Jcc.540080710 |
0.379 |
|
| 1984 |
Corey E, Ponder JW. Stereochemistry of the hygrolidins Tetrahedron Letters. 25: 4325-4328. DOI: 10.1016/S0040-4039(01)81429-5 |
0.393 |
|
| 1984 |
Corey E, De B, Ponder JW, Berg JM. The stereochemistry and biosynthesis of hybridalactone, an eicosanoid from Tetrahedron Letters. 25: 1015-1018. DOI: 10.1016/S0040-4039(01)80088-5 |
0.366 |
|
| 1980 |
Corey E, Ponder JW, Ulrich P. Synthesis of a stable analog of thromboxane A2 with methylene replacing the 9,11-bridging oxygen Tetrahedron Letters. 21: 137-140. DOI: 10.1016/S0040-4039(00)71395-5 |
0.342 |
|
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