Jay W. Ponder - Publications

Affiliations: 
Washington University, Saint Louis, St. Louis, MO 
Area:
General Biophysics, Condensed Matter Physics, Biomedical Engineering

49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.96
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  0.44
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  1
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  1
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  0.88
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  1
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  1
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  1
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  1
2016 Pickard FC, König G, Tofoleanu F, Lee J, Simmonett AC, Shao Y, Ponder JW, Brooks BR. Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections. Journal of Computer-Aided Molecular Design. PMID 27646286 DOI: 10.1007/s10822-016-9955-7  1
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  1
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  1
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  0.96
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  1
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  1
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  1
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  1
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  1
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  1
2014 Liu C, Ponder JW, Marshall GR. Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence. Proteins. 82: 3043-61. PMID 25116421 DOI: 10.1002/prot.24665  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.88
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  1
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  1
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  1
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  1
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  1
2001 Frieden C, Huang ES, Ponder JW. Turn scanning. Experimental and theoretical approaches to the role of turns. Methods in Molecular Biology (Clifton, N.J.). 168: 133-158. PMID 11357623  1
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  1
2000 Hart RK, Pappu RV, Ponder JW. Exploring the Similarities between Potential Smoothing and Simulated Annealing Journal of Computational Chemistry. 21: 531-552.  1
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  1
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  1
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  1
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  1
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  1
1998 Kisselev OG, Kao J, Ponder JW, Fann YC, Gautam N, Marshall GR. Light-activated rhodopsin induces structural binding motif in G protein alpha subunit. Proceedings of the National Academy of Sciences of the United States of America. 95: 4270-5. PMID 9539726 DOI: 10.1073/pnas.95.8.4270  1
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.  1
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  1
1995 York JD, Ponder JW, Majerus PW. Definition of a metal-dependent/Li(+)-inhibited phosphomonoesterase protein family based upon a conserved three-dimensional core structure. Proceedings of the National Academy of Sciences of the United States of America. 92: 5149-53. PMID 7761465 DOI: 10.1073/pnas.92.11.5149  1
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  1
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  1
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