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Evaluation of neurobehavioral abnormalities and immunotoxicity in response to oral imidacloprid exposure in domestic chickens (Gallus gallus domesticus).

Franzen-Klein D, Jankowski M, Roy CL, Nguyen-Phuc H, Chen D, Neuman-Lee L, Redig P, Ponder J.

J Toxicol Environ Health A. 2020 Jan 17;83(2):45-65. doi: 10.1080/15287394.2020.1723154. Epub 2020 Feb 5.


Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Patients with Acute Myeloid Leukemia.

Pei S, Pollyea DA, Gustafson A, Stevens BM, Minhajuddin M, Fu R, Riemondy KA, Gillen AE, Sheridan RM, Kim J, Costello JC, Amaya ML, Inguva A, Winters A, Ye H, Krug A, Jones CL, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers JR, Ashton JM, Nemkov T, D'Alessandro A, Gutman JA, Ramsey HE, Savona MR, Smith CA, Jordan CT.

Cancer Discov. 2020 Jan 23. doi: 10.1158/2159-8290.CD-19-0710. [Epub ahead of print]


Distraction Osteogenesis in Two Wild Raptors.

Bueno I, Anderson G, Willette M, Redig PT, Ponder J.

J Avian Med Surg. 2019 Dec 9;33(4):427-436. doi: 10.1647/2018-384.


Auditory performance in bald eagles and red-tailed hawks: a comparative study of hearing in diurnal raptors.

McGee J, Nelson PB, Ponder JB, Marr J, Redig P, Walsh EJ.

J Comp Physiol A Neuroethol Sens Neural Behav Physiol. 2019 Dec;205(6):793-811. doi: 10.1007/s00359-019-01367-9. Epub 2019 Sep 13.


Multi-scale availability of neonicotinoid-treated seed for wildlife in an agricultural landscape during spring planting.

Roy CL, Coy PL, Chen D, Ponder J, Jankowski M.

Sci Total Environ. 2019 Sep 10;682:271-281. doi: 10.1016/j.scitotenv.2019.05.010. Epub 2019 May 4.


Classical Pauli repulsion: An anisotropic, atomic multipole model.

Rackers JA, Ponder JW.

J Chem Phys. 2019 Feb 28;150(8):084104. doi: 10.1063/1.5081060.


Balancing Charge Storage and Mobility in an Oligo(Ether) Functionalized Dioxythiophene Copolymer for Organic- and Aqueous- Based Electrochemical Devices and Transistors.

Savagian LR, Österholm AM, Ponder JF Jr, Barth KJ, Rivnay J, Reynolds JR.

Adv Mater. 2018 Dec;30(50):e1804647. doi: 10.1002/adma.201804647. Epub 2018 Oct 14.


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

Laury ML, Wang Z, Gordon AS, Ponder JW.

J Comput Aided Mol Des. 2018 Oct;32(10):1087-1095. doi: 10.1007/s10822-018-0147-5. Epub 2018 Oct 15.


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

Rackers JA, Liu C, Ren P, Ponder JW.

J Chem Phys. 2018 Aug 28;149(8):084115. doi: 10.1063/1.5030434.


Tinker 8: Software Tools for Molecular Design.

Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW.

J Chem Theory Comput. 2018 Oct 9;14(10):5273-5289. doi: 10.1021/acs.jctc.8b00529. Epub 2018 Sep 19.


MMB triazole analogs are potent NF-κB inhibitors and anti-cancer agents against both hematological and solid tumor cells.

Janganati V, Ponder J, Balasubramaniam M, Bhat-Nakshatri P, Bar EE, Nakshatri H, Jordan CT, Crooks PA.

Eur J Med Chem. 2018 Sep 5;157:562-581. doi: 10.1016/j.ejmech.2018.08.010. Epub 2018 Aug 10.


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

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.

Chem Sci. 2017 Nov 27;9(4):956-972. doi: 10.1039/c7sc04531j. eCollection 2018 Jan 28.


AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

Zhang C, Lu C, Jing Z, Wu C, Piquemal JP, Ponder JW, Ren P.

J Chem Theory Comput. 2018 Apr 10;14(4):2084-2108. doi: 10.1021/acs.jctc.7b01169. Epub 2018 Mar 6.


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

Harger M, Li D, Wang Z, Dalby K, Lagardère L, Piquemal JP, Ponder J, Ren P.

J Comput Chem. 2017 Sep 5;38(23):2047-2055. doi: 10.1002/jcc.24853. Epub 2017 Jun 10.


Succinamide derivatives of melampomagnolide B and their anti-cancer activities.

Janganati V, Ponder J, Thakkar S, Jordan CT, Crooks PA.

Bioorg Med Chem. 2017 Jul 15;25(14):3694-3705. doi: 10.1016/j.bmc.2017.05.008. Epub 2017 May 8.


Indole carboxylic acid esters of melampomagnolide B are potent anticancer agents against both hematological and solid tumor cells.

Bommagani S, Ponder J, Penthala NR, Janganati V, Jordan CT, Borrelli MJ, Crooks PA.

Eur J Med Chem. 2017 Aug 18;136:393-405. doi: 10.1016/j.ejmech.2017.05.031. Epub 2017 May 11.


Resiliency in the Face of Adversity.

Ponder JL.

J Christ Nurs. 2017 Apr/Jun;34(2):130. doi: 10.1097/CNJ.0000000000000366. No abstract available.


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

Aviat F, Levitt A, Stamm B, Maday Y, Ren P, Ponder JW, Lagardère L, Piquemal JP.

J Chem Theory Comput. 2017 Jan 10;13(1):180-190. doi: 10.1021/acs.jctc.6b00981. Epub 2016 Dec 8.


Identification of a melampomagnolide B analog as a potential lead molecule for treatment of acute myelogenous leukemia.

Albayati ZAF, Janganati V, Chen Z, Ponder J, Breen PJ, Jordan CT, Crooks PA.

Bioorg Med Chem. 2017 Feb 1;25(3):1235-1241. doi: 10.1016/j.bmc.2016.12.036. Epub 2016 Dec 26.


Raptor Acupuncture for Treating Chronic Degenerative Joint Disease.

Choi KH, Buhl G, Ponder J.

J Acupunct Meridian Stud. 2016 Dec;9(6):330-334. doi: 10.1016/j.jams.2016.09.020. Epub 2016 Oct 4.


Autonomy and Firefighting: Perceived Competence and Stress.

Chiang ES, Baley J, Ponder J, Padilla MA.

J Occup Environ Med. 2016 Dec;58(12):1223-1230.


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

Rackers JA, Wang Q, Liu C, Piquemal JP, Ren P, Ponder JW.

Phys Chem Chem Phys. 2016 Dec 21;19(1):276-291. doi: 10.1039/c6cp06017j.


An empirical extrapolation scheme for efficient treatment of induced dipoles.

Simmonett AC, Pickard FC 4th, Ponder JW, Brooks BR.

J Chem Phys. 2016 Oct 28;145(16):164101.


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

Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK.

J Chem Phys. 2016 Sep 28;145(12):124106.


Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections.

Pickard FC 4th, König G, Tofoleanu F, Lee J, Simmonett AC, Shao Y, Ponder JW, Brooks BR.

J Comput Aided Mol Des. 2016 Nov;30(11):1087-1100. doi: 10.1007/s10822-016-9955-7. Epub 2016 Sep 19.


Advanced Potential Energy Surfaces for Molecular Simulation.

Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails J, Zeng Q, Case DA, Eastman P, Wang LP, Essex JW, Head-Gordon M, Pande VS, Ponder JW, Shao Y, Skylaris CK, Todorov IT, Tuckerman ME, Head-Gordon T.

J Phys Chem B. 2016 Sep 22;120(37):9811-32. doi: 10.1021/acs.jpcb.6b06414. Review.


Chemoenzymatic synthesis and antileukemic activity of novel C9- and C14-functionalized parthenolide analogs.

Tyagi V, Alwaseem H, O'Dwyer KM, Ponder J, Li QY, Jordan CT, Fasan R.

Bioorg Med Chem. 2016 Sep 1;24(17):3876-3886. doi: 10.1016/j.bmc.2016.06.028. Epub 2016 Jun 16.


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

Bell DR, Qi R, Jing Z, Xiang JY, Mejias C, Schnieders MJ, Ponder JW, Ren P.

Phys Chem Chem Phys. 2016 Nov 9;18(44):30261-30269. doi: 10.1039/c6cp02509a.


Solution Processed PEDOT Analogues in Electrochemical Supercapacitors.

Österholm AM, Ponder JF Jr, Kerszulis JA, Reynolds JR.

ACS Appl Mater Interfaces. 2016 Jun 1;8(21):13492-8. doi: 10.1021/acsami.6b02434. Epub 2016 May 19.


Design of Hybrid Electrochromic Materials with Large Electrical Modulation of Plasmonic Resonances.

Ledin PA, Jeon JW, Geldmeier JA, Ponder JF Jr, Mahmoud MA, El-Sayed M, Reynolds JR, Tsukruk VV.

ACS Appl Mater Interfaces. 2016 May 25;8(20):13064-75. doi: 10.1021/acsami.6b02953. Epub 2016 May 11.


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

Narth C, Lagardère L, Polack É, Gresh N, Wang Q, Bell DR, Rackers JA, Ponder JW, Ren PY, Piquemal JP.

J Comput Chem. 2016 Feb 15;37(5):494-506. doi: 10.1002/jcc.24257.


Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate.

Zhang C, Lu C, Wang Q, Ponder JW, Ren P.

J Chem Theory Comput. 2015 Nov 10;11(11):5326-39. doi: 10.1021/acs.jctc.5b00562. Epub 2015 Oct 28.


Dimers of Melampomagnolide B Exhibit Potent Anticancer Activity against Hematological and Solid Tumor Cells.

Janganati V, Ponder J, Jordan CT, Borrelli MJ, Penthala NR, Crooks PA.

J Med Chem. 2015 Nov 25;58(22):8896-906. doi: 10.1021/acs.jmedchem.5b01187. Epub 2015 Nov 16.


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

Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P.

J Chem Theory Comput. 2015 Jun 9;11(6):2609-2618. Epub 2015 Apr 28.


High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

Kuster DJ, Liu C, Fang Z, Ponder JW, Marshall GR.

PLoS One. 2015 Apr 20;10(4):e0123146. doi: 10.1371/journal.pone.0123146. eCollection 2015.


Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Laury ML, Wang LP, Pande VS, Head-Gordon T, Ponder JW.

J Phys Chem B. 2015 Jul 23;119(29):9423-9437. doi: 10.1021/jp510896n. Epub 2015 Feb 26.


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

Liu C, Ponder JW, Marshall GR.

Proteins. 2014 Nov;82(11):3043-61. doi: 10.1002/prot.24665. Epub 2014 Sep 20.


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

Xiang JY, Ponder JW.

J Chem Theory Comput. 2014;10(1):298-311.


Aldose reductase inhibition prevents endotoxin-induced inflammatory responses in retinal microglia.

Chang KC, Ponder J, Labarbera DV, Petrash JM.

Invest Ophthalmol Vis Sci. 2014 May 2;55(5):2853-61. doi: 10.1167/iovs.13-13487.


Design of an amide N-glycoside derivative of β-glucogallin: a stable, potent, and specific inhibitor of aldose reductase.

Li L, Chang KC, Zhou Y, Shieh B, Ponder J, Abraham AD, Ali H, Snow A, Petrash JM, LaBarbera DV.

J Med Chem. 2014 Jan 9;57(1):71-7. doi: 10.1021/jm401311d. Epub 2013 Dec 23.


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

Shi Y, Xia Z, Zhang J, Best R, Wu C, Ponder JW, Ren P.

J Chem Theory Comput. 2013;9(9):4046-4063.


Systematic improvement of a classical molecular model of water.

Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS.

J Phys Chem B. 2013 Aug 29;117(34):9956-72. doi: 10.1021/jp403802c. Epub 2013 Aug 14.


Beta-glucogallin reduces the expression of lipopolysaccharide-induced inflammatory markers by inhibition of aldose reductase in murine macrophages and ocular tissues.

Chang KC, Laffin B, Ponder J, Enzsöly A, Németh J, LaBarbera DV, Petrash JM.

Chem Biol Interact. 2013 Feb 25;202(1-3):283-7. doi: 10.1016/j.cbi.2012.12.001. Epub 2012 Dec 15.


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

Xiang JY, Ponder JW.

J Comput Chem. 2013 Apr 5;34(9):739-49. doi: 10.1002/jcc.23190. Epub 2012 Dec 5.


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

Zheng X, Wu C, Ponder JW, Marshall GR.

J Am Chem Soc. 2012 Sep 26;134(38):15970-8. Epub 2012 Sep 17.


Assessment of anesthesia provides' opinions regarding pediatric induction practices in the state of Oklahoma.

de Armendi AJ, Mayhew JF, Shukry M, Seshachar A, Ponder J, Martinez M, Strong P, Cure JA.

J Okla State Med Assoc. 2012 Mar;105(3):92-6.


The isolation and characterization of β-glucogallin as a novel aldose reductase inhibitor from Emblica officinalis.

Puppala M, Ponder J, Suryanarayana P, Reddy GB, Petrash JM, LaBarbera DV.

PLoS One. 2012;7(4):e31399. doi: 10.1371/journal.pone.0031399. Epub 2012 Apr 2.


Neoamphimedine circumvents metnase-enhanced DNA topoisomerase IIα activity through ATP-competitive inhibition.

Ponder J, Yoo BH, Abraham AD, Li Q, Ashley AK, Amerin CL, Zhou Q, Reid BG, Reigan P, Hromas R, Nickoloff JA, LaBarbera DV.

Mar Drugs. 2011;9(11):2397-408. doi: 10.3390/md9112397. Epub 2011 Nov 18.


Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

Ren P, Wu C, Ponder JW.

J Chem Theory Comput. 2011 Oct 11;7(10):3143-3161.


MSCALE: A General Utility for Multiscale Modeling.

Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW, Brooks BR.

J Chem Theory Comput. 2011 Apr 12;7(4):1208-1219.

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