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Using AMBER18 for Relative Free Energy Calculations.

Song LF, Lee TS, Zhu C, York DM, Merz KM Jr.

J Chem Inf Model. 2019 Jun 20. doi: 10.1021/acs.jcim.9b00105. [Epub ahead of print]


Measuring the permeability of thin solid layers of natural waxes.

York DW, Collins S, Rantape M.

J Colloid Interface Sci. 2019 Sep 1;551:270-282. doi: 10.1016/j.jcis.2019.03.104. Epub 2019 Apr 15.


An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes.

Bevilacqua PC, Harris ME, Piccirilli JA, Gaines C, Ganguly A, Kostenbader K, Ekesan Ş, York DM.

ACS Chem Biol. 2019 Jun 21;14(6):1068-1076. doi: 10.1021/acschembio.9b00202. Epub 2019 Jun 7.


Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation.

Ekesan Ş, York DM.

J Phys Chem B. 2019 Jun 6;123(22):4611-4624. doi: 10.1021/acs.jpcb.8b11923. Epub 2019 May 3.


Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction.

Li X, York DM, Meyer MP.

J Phys Chem A. 2019 May 2;123(17):3647-3654. doi: 10.1021/acs.jpca.9b00172. Epub 2019 Apr 22.


Metastatic immune infiltrates correlate with those of the primary tumour in canine osteosarcoma.

Withers SS, York D, Choi JW, Woolard KD, Laufer-Amorim R, Sparger EE, Burton JH, McSorley SJ, Monjazeb AM, Murphy WJ, Canter RJ, Rebhun RB.

Vet Comp Oncol. 2019 Jan 25. doi: 10.1111/vco.12459. [Epub ahead of print]


Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory.

Giambaşu GM, Case DA, York DM.

J Am Chem Soc. 2019 Feb 13;141(6):2435-2445. doi: 10.1021/jacs.8b11474. Epub 2019 Jan 29.


On the convergence of multi-scale free energy simulations.

König G, Brooks BR, Thiel W, York DM.

Mol Simul. 2018;44(13-14):1062-1081. doi: 10.1080/08927022.2018.1475741. Epub 2018 May 30.


Fatal injuries among Hispanic workers in the U.S. construction industry: Findings from FACE investigation reports.

Al-Bayati AJ, York DD.

J Safety Res. 2018 Dec;67:117-123. doi: 10.1016/j.jsr.2018.09.007. Epub 2018 Oct 4.


Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 which contributes to Robinow-like syndrome in Bulldogs and related screw tail dog breeds.

Mansour TA, Lucot K, Konopelski SE, Dickinson PJ, Sturges BK, Vernau KL, Choi S, Stern JA, Thomasy SM, Döring S, Verstraete FJM, Johnson EG, York D, Rebhun RB, Ho HH, Brown CT, Bannasch DL.

PLoS Genet. 2018 Dec 6;14(12):e1007850. doi: 10.1371/journal.pgen.1007850. eCollection 2018 Dec.


A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM.

Molecules. 2018 Oct 19;23(10). pii: E2695. doi: 10.3390/molecules23102695.


Development and Pilot Testing of a Computerized Asthma Kiosk to Initiate Chronic Asthma Care in a Pediatric Emergency Department.

Kwok MY, Bakken SR, Pusic MV, York D, Pahalyants V, Ye C, Javed K, Dayan PS.

Pediatr Emerg Care. 2018 Oct;34(10):e190-e195. doi: 10.1097/PEC.0000000000001630.


GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.

Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg A, Case DA, Walker RC, York DM.

J Chem Inf Model. 2018 Oct 22;58(10):2043-2050. doi: 10.1021/acs.jcim.8b00462. Epub 2018 Sep 25.


Asthma-Related Educational Needs of Families With Children With Asthma in an Urban Pediatric Emergency Department.

Kwok MY, Pusic MV, Cabrera KI, York DV, Lee J, Evans D.

Pediatr Emerg Care. 2018 Sep;34(9):636-640. doi: 10.1097/PEC.0000000000001607.


Association of macrophage and lymphocyte infiltration with outcome in canine osteosarcoma.

Withers SS, Skorupski KA, York D, Choi JW, Woolard KD, Laufer-Amorim R, Sparger EE, Rodriguez CO, McSorley SJ, Monjazeb AM, Murphy WJ, Canter RJ, Rebhun RB.

Vet Comp Oncol. 2019 Mar;17(1):49-60. doi: 10.1111/vco.12444. Epub 2018 Sep 19.


In vitro and in vivo activity of liposome-encapsulated curcumin for naturally occurring canine cancers.

Withers SS, York D, Johnson E, Al-Nadaf S, Skorupski KA, Rodriguez CO Jr, Burton JH, Guerrero T, Sein K, Wittenburg L, Rebhun RB.

Vet Comp Oncol. 2018 Dec;16(4):571-579. doi: 10.1111/vco.12424. Epub 2018 Aug 8.


Human energy expenditure modelling research.

York D, Pietrobelli A.

Obes Rev. 2018 Sep;19(9):1175-1176. doi: 10.1111/obr.12722. Epub 2018 Jul 27. No abstract available.


Accuracy and safety of dry needle placement in the piriformis muscle in cadavers.

Kearns G, Gilbert KK, Allen B, Sizer PS Jr, Brismée JM, Pendergrass T, Lierly M, York D.

J Man Manip Ther. 2018 May;26(2):89-96. doi: 10.1080/10669817.2017.1346745. Epub 2017 Jul 6.


Comparative Cytogenetic Analysis of Dog and Human Choroid Plexus Tumors Defines Syntenic Regions of Genomic Loss.

Ancona D, York D, Higgins RJ, Bannasch D, Dickinson PJ.

J Neuropathol Exp Neurol. 2018 May 1;77(5):413-419. doi: 10.1093/jnen/nly020.


A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method.

Giese TJ, York DM.

J Chem Theory Comput. 2018 Mar 13;14(3):1564-1582. doi: 10.1021/acs.jctc.7b01175. Epub 2018 Feb 7.


A Learning Collaborative Approach to Improve Primary Care STI Screening.

McKee MD, Alderman E, York DV, Blank AE, Briggs RD, Hoidal KES, Kus C, Lechuga C, Mann M, Meissner P, Patel N, Racine AD.

Clin Pediatr (Phila). 2018 Jul;57(8):895-903. doi: 10.1177/0009922817733702. Epub 2017 Oct 13.


Kinetic Isotope Effect Analysis of RNA 2'-O-Transphosphorylation.

Harris ME, York DM, Piccirilli JA, Anderson VE.

Methods Enzymol. 2017;596:433-457. doi: 10.1016/bs.mie.2017.07.017. Epub 2017 Sep 5.


Quantum mechanical force fields for condensed phase molecular simulations.

Giese TJ, York DM.

J Phys Condens Matter. 2017 Sep 27;29(38):383002. doi: 10.1088/1361-648X/aa7c5c. Epub 2017 Aug 17.


Production of Concentrated Pickering Emulsions with Narrow Size Distributions Using Stirred Cell Membrane Emulsification.

Manga MS, York DW.

Langmuir. 2017 Sep 12;33(36):9050-9056. doi: 10.1021/acs.langmuir.7b01812. Epub 2017 Aug 25.


A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.

Huang M, Dissanayake T, Kuechler E, Radak BK, Lee TS, Giese TJ, York DM.

J Chem Theory Comput. 2017 Sep 12;13(9):3975-3984. doi: 10.1021/acs.jctc.7b00161. Epub 2017 Aug 17.


Model for the Functional Active State of the TS Ribozyme from Molecular Simulation.

Gaines CS, York DM.

Angew Chem Int Ed Engl. 2017 Oct 16;56(43):13392-13395. doi: 10.1002/anie.201705608. Epub 2017 Sep 8.


Evaluation of P16 expression in canine appendicular osteosarcoma.

Murphy BG, Mok MY, York D, Rebhun R, Woolard KD, Hillman C, Dickinson P, Skorupski K.

BMC Vet Res. 2017 Jun 20;13(1):189. doi: 10.1186/s12917-017-1113-5.


Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration.

Lee TS, Hu Y, Sherborne B, Guo Z, York DM.

J Chem Theory Comput. 2017 Jul 11;13(7):3077-3084. doi: 10.1021/acs.jctc.7b00102. Epub 2017 Jun 23.


Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations.

Chen H, Giese TJ, Golden BL, York DM.

Biochemistry. 2017 Jun 20;56(24):2985-2994. doi: 10.1021/acs.biochem.6b01192. Epub 2017 Jun 12.


Expression and targeting of transcription factor ATF5 in dog gliomas.

York D, Sproul CD, Chikere N, Dickinson PJ, Angelastro JM.

Vet Comp Oncol. 2018 Mar;16(1):102-107. doi: 10.1111/vco.12317. Epub 2017 May 8.


A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.

Lee TS, Radak BK, Harris ME, York DM.

ACS Catal. 2016;6(3):1853-1869. Epub 2016 Feb 1.


Communication skills training for radiation therapists: preparing patients for radiation therapy.

Halkett G, O'Connor M, Aranda S, Jefford M, Merchant S, York D, Miller L, Schofield P.

J Med Radiat Sci. 2016 Dec;63(4):232-241. doi: 10.1002/jmrs.171. Epub 2016 Apr 21.


Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.

Janowski PA, Moriarty NW, Kelley BP, Case DA, York DM, Adams PD, Warren GL.

Acta Crystallogr D Struct Biol. 2016 Sep;72(Pt 9):1062-72. doi: 10.1107/S2059798316012225. Epub 2016 Aug 31.


The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

Hu Y, Sherborne B, Lee TS, Case DA, York DM, Guo Z.

J Comput Aided Mol Des. 2016 Jul;30(7):533-9. doi: 10.1007/s10822-016-9920-5. Epub 2016 Aug 1.


Enrofloxacin enhances the effects of chemotherapy in canine osteosarcoma cells with mutant and wild-type p53.

York D, Withers SS, Watson KD, Seo KW, Rebhun RB.

Vet Comp Oncol. 2017 Sep;15(3):1087-1100. doi: 10.1111/vco.12250. Epub 2016 Jun 23.


Chromosomal Aberrations in Canine Gliomas Define Candidate Genes and Common Pathways in Dogs and Humans.

Dickinson PJ, York D, Higgins RJ, LeCouteur RA, Joshi N, Bannasch D.

J Neuropathol Exp Neurol. 2016 Jul;75(7):700-10. doi: 10.1093/jnen/nlw042. Epub 2016 May 31.


Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

Giese TJ, York DM.

J Chem Theory Comput. 2016 Jun 14;12(6):2611-32. doi: 10.1021/acs.jctc.6b00198. Epub 2016 May 26.


Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus.

Truvé K, Dickinson P, Xiong A, York D, Jayashankar K, Pielberg G, Koltookian M, Murén E, Fuxelius HH, Weishaupt H, Swartling FJ, Andersson G, Hedhammar Å, Bongcam-Rudloff E, Forsberg-Nilsson K, Bannasch D, Lindblad-Toh K.

PLoS Genet. 2016 May 12;12(5):e1006000. doi: 10.1371/journal.pgen.1006000. eCollection 2016 May.


VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.

Kuechler ER, Giese TJ, York DM.

J Chem Phys. 2016 Apr 28;144(16):164115. doi: 10.1063/1.4946779.


Measurements of Submicron Particle Adsorption and Particle Film Elasticity at Oil-Water Interfaces.

Manga MS, Hunter TN, Cayre OJ, York DW, Reichert MD, Anna SL, Walker LM, Williams RA, Biggs SR.

Langmuir. 2016 May 3;32(17):4125-33. doi: 10.1021/acs.langmuir.5b04586. Epub 2016 Apr 22.


Generating aldehyde-tagged antibodies with high titers and high formylglycine yields by supplementing culture media with copper(II).

York D, Baker J, Holder PG, Jones LC, Drake PM, Barfield RM, Bleck GT, Rabuka D.

BMC Biotechnol. 2016 Feb 24;16:23. doi: 10.1186/s12896-016-0254-0.


Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation.

Gaines CS, York DM.

J Am Chem Soc. 2016 Mar 9;138(9):3058-65. doi: 10.1021/jacs.5b12061. Epub 2016 Feb 25.


Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+).

Zhang S, Gu H, Chen H, Strong E, Ollie EW, Kellerman D, Liang D, Miyagi M, Anderson VE, Piccirilli JA, York DM, Harris ME.

Chem Commun (Camb). 2016 Mar 25;52(24):4462-5. doi: 10.1039/c5cc10212j.


Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations.

Kuechler ER, Giese TJ, York DM.

J Chem Phys. 2015 Dec 21;143(23):234111. doi: 10.1063/1.4937166.


Measles Virus Neutralizing Antibody Response, Cell-Mediated Immunity, and Immunoglobulin G Antibody Avidity Before and After Receipt of a Third Dose of Measles, Mumps, and Rubella Vaccine in Young Adults.

Fiebelkorn AP, Coleman LA, Belongia EA, Freeman SK, York D, Bi D, Kulkarni A, Audet S, Mercader S, McGrew M, Hickman CJ, Bellini WJ, Shivakoti R, Griffin DE, Beeler J.

J Infect Dis. 2016 Apr 1;213(7):1115-23. doi: 10.1093/infdis/jiv555. Epub 2015 Nov 23.


Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids.

Panteva MT, Giambaşu GM, York DM.

J Phys Chem B. 2015 Dec 17;119(50):15460-70. doi: 10.1021/acs.jpcb.5b10423. Epub 2015 Dec 3.


Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations.

Radak BK, Romanus M, Lee TS, Chen H, Huang M, Treikalis A, Balasubramanian V, Jha S, York DM.

J Chem Theory Comput. 2015 Feb 10;11(2):373-7. doi: 10.1021/ct500776j.


An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

Sengupta RN, Van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D.

RNA. 2016 Jan;22(1):32-48. doi: 10.1261/rna.053710.115. Epub 2015 Nov 13.


Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.

Gebala M, Giambaşu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D.

J Am Chem Soc. 2015 Nov 25;137(46):14705-15. doi: 10.1021/jacs.5b08395. Epub 2015 Nov 12.


Competitive interaction of monovalent cations with DNA from 3D-RISM.

Giambaşu GM, Gebala MK, Panteva MT, Luchko T, Case DA, York DM.

Nucleic Acids Res. 2015 Sep 30;43(17):8405-15. doi: 10.1093/nar/gkv830. Epub 2015 Aug 24.

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