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Curved or linear? Predicting the 3-dimensional structure of α-helical antimicrobial peptides in an amphipathic environment.

van den Bergen G, Stroet M, Caron B, Poger D, Mark AE.

FEBS Lett. 2019 Dec 3. doi: 10.1002/1873-3468.13705. [Epub ahead of print]


Adult validation of a self-administered tablet audiometer.

Bastianelli M, Mark AE, McAfee A, Schramm D, Lefrançois R, Bromwich M.

J Otolaryngol Head Neck Surg. 2019 Nov 7;48(1):59. doi: 10.1186/s40463-019-0385-0.


Nordic walking and standard exercise therapy in patients with chronic heart failure: A randomised controlled trial comparison.

Prince SA, Wooding E, Mielniczuk L, Pipe AL, Chan KL, Keast ML, Harris J, Tulloch HE, Mark AE, Cotie LM, Wells GA, Reid RD.

Eur J Prev Cardiol. 2019 Nov;26(16):1790-1794. doi: 10.1177/2047487319871215. Epub 2019 Aug 19. No abstract available.


Effect of Triclosan and Chloroxylenol on Bacterial Membranes.

Poger D, Mark AE.

J Phys Chem B. 2019 Jun 27;123(25):5291-5301. doi: 10.1021/acs.jpcb.9b02588. Epub 2019 Jun 18.


Response of microbial membranes to butanol: interdigitation vs. disorder.

Guo J, Ho JCS, Chin H, Mark AE, Zhou C, Kjelleberg S, Liedberg B, Parikh AN, Cho NJ, Hinks J, Mu Y, Seviour T.

Phys Chem Chem Phys. 2019 Jun 5;21(22):11903-11915. doi: 10.1039/c9cp01469a.


Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.

Engler MS, Caron B, Veen L, Geerke DP, Mark AE, Klau GW.

Algorithms Mol Biol. 2019 Feb 5;14:1. doi: 10.1186/s13015-019-0138-7. eCollection 2019.


Could Cardiolipin Protect Membranes against the Action of Certain Antimicrobial Peptides? Aurein 1.2, a Case Study.

Poger D, Pöyry S, Mark AE.

ACS Omega. 2018 Dec 31;3(12):16453-16464. doi: 10.1021/acsomega.8b02710. Epub 2018 Dec 3.


Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations.

Subramanian N, Schumann-Gillett A, Mark AE, O'Mara ML.

J Chem Inf Model. 2019 May 28;59(5):2287-2298. doi: 10.1021/acs.jcim.8b00624. Epub 2019 Jan 2.


Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane.

Stroet M, Caron B, Visscher KM, Geerke DP, Malde AK, Mark AE.

J Chem Theory Comput. 2018 Nov 13;14(11):5834-5845. doi: 10.1021/acs.jctc.8b00768. Epub 2018 Oct 22.


Impact of health care reform on enrolment of immigrants in primary care in Ontario, Canada.

Batista R, Pottie KC, Dahrouge S, Manuel DG, Tanuseputro P, Mark AE, Ng E.

Fam Pract. 2019 Jul 31;36(4):445-451. doi: 10.1093/fampra/cmy082.


Morphology of a Bulk Heterojunction Photovoltaic Cell with Low Donor Concentration.

Lee T, Sanzogni A, Zhangzhou N, Burn PL, Mark AE.

ACS Appl Mater Interfaces. 2018 Sep 26;10(38):32413-32419. doi: 10.1021/acsami.8b10321. Epub 2018 Sep 11.


Imaging of cortical oxygen tension and blood flow following targeted photothrombotic stroke.

Sullender CT, Mark AE, Clark TA, Esipova TV, Vinogradov SA, Jones TA, Dunn AK.

Neurophotonics. 2018 Jul;5(3):035003. doi: 10.1117/1.NPh.5.3.035003. Epub 2018 Jul 27.


Dilating and fracturing side struts of open cell stents frequently used in pediatric cardiac interventions-An in vitro study.

Krasemann T, Kruit MN, van der Mark AE, Zeggelaar M, Dalinghaus M, van Beynum IM.

J Interv Cardiol. 2018 Dec;31(6):834-840. doi: 10.1111/joic.12549. Epub 2018 Aug 8.


Predicting the Prevalence of Alternative Warfarin Tautomers in Solution.

Malde AK, Stroet M, Caron B, Visscher KM, Mark AE.

J Chem Theory Comput. 2018 Aug 14;14(8):4405-4415. doi: 10.1021/acs.jctc.8b00453. Epub 2018 Jul 25.


Hepatitis C Testing, Status and Treatment among Marginalized People Who Use Drugs in an Inner City Setting: An Observational Cohort Study.

Boucher LM, Bayoumi AM, Mark AE, Cooper C, Martin A, Marshall Z, Boyd R, Oickle P, Diliso N, Pineau D, Renaud B, LeBlanc S, Tyndall M, Lee OM, Kendall CE.

Subst Use Misuse. 2019;54(1):18-30. doi: 10.1080/10826084.2018.1485699. Epub 2018 Jun 22.


Assessing Timely Presentation to Care Among People Diagnosed with HIV During Hospital Admission: A Population-Based Study in Ontario, Canada.

Kendall CE, Shoemaker ES, Raboud J, Mark AE, Bayoumi AM, Burchell AN, Loutfy M, Rourke SB, Liddy CE, Rosenes R, Rogers T, Antoniou T.

AIDS Behav. 2018 Aug;22(8):2575-2583. doi: 10.1007/s10461-018-2063-z.


Effect of Binding on Enantioselectivity of Epoxide Hydrolase.

Zaugg J, Gumulya Y, Bodén M, Mark AE, Malde AK.

J Chem Inf Model. 2018 Mar 26;58(3):630-640. doi: 10.1021/acs.jcim.7b00353. Epub 2018 Feb 20.


The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment.

Condic-Jurkic K, Subramanian N, Mark AE, O'Mara ML.

PLoS One. 2018 Jan 25;13(1):e0191882. doi: 10.1371/journal.pone.0191882. eCollection 2018.


Developments in Glycopeptide Antibiotics.

Blaskovich MAT, Hansford KA, Butler MS, Jia Z, Mark AE, Cooper MA.

ACS Infect Dis. 2018 May 11;4(5):715-735. doi: 10.1021/acsinfecdis.7b00258. Epub 2018 Feb 19.


Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach.

Stroet M, Koziara KB, Malde AK, Mark AE.

J Chem Theory Comput. 2017 Dec 12;13(12):6201-6212. doi: 10.1021/acs.jctc.7b00800. Epub 2017 Nov 21.


The Molecular Origin of Anisotropic Emission in an Organic Light-Emitting Diode.

Lee T, Caron B, Stroet M, Huang DM, Burn PL, Mark AE.

Nano Lett. 2017 Oct 11;17(10):6464-6468. doi: 10.1021/acs.nanolett.7b03528. Epub 2017 Sep 18.


Validation of Molecular Simulation: An Overview of Issues.

van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ.

Angew Chem Int Ed Engl. 2018 Jan 22;57(4):884-902. doi: 10.1002/anie.201702945. Epub 2017 Dec 27. Review.


Erratum to: A cohort study examining emergency department visits and hospital admissions among people who use drugs in Ottawa, Canada.

Kendall CE, Boucher LM, Mark AE, Martin A, Marshall Z, Boyd R, Oickle P, Diliso N, Pineau D, Renaud B, Rose T, LeBlanc S, Tyndall M, Lee OM, Bayoumi AM.

Harm Reduct J. 2017 Jul 3;14(1):42. doi: 10.1186/s12954-017-0169-7. No abstract available.


A potential new, stable state of the E-cadherin strand-swapped dimer in solution.

Schumann-Gillett A, Mark AE, Deplazes E, O'Mara ML.

Eur Biophys J. 2018 Jan;47(1):59-67. doi: 10.1007/s00249-017-1229-3. Epub 2017 Jun 15.


A cohort study examining emergency department visits and hospital admissions among people who use drugs in Ottawa, Canada.

Kendall CE, Boucher LM, Mark AE, Martin A, Marshall Z, Boyd R, Oickle P, Diliso N, Pineau D, Renaud B, Rose T, LeBlanc S, Tyndall M, Lee OM, Bayoumi AM.

Harm Reduct J. 2017 May 12;14(1):16. doi: 10.1186/s12954-017-0143-4. Erratum in: Harm Reduct J. 2017 Jul 3;14 (1):42.


Real Cost of Speed: The Effect of a Time-Saving Multiple-Time-Stepping Algorithm on the Accuracy of Molecular Dynamics Simulations.

Reißer S, Poger D, Stroet M, Mark AE.

J Chem Theory Comput. 2017 Jun 13;13(6):2367-2372. doi: 10.1021/acs.jctc.7b00178. Epub 2017 May 26.


Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study.

Corbett MSP, Mark AE, Poger D.

Biophys J. 2017 Feb 28;112(4):595-604. doi: 10.1016/j.bpj.2016.12.042.


Elucidating the Spatial Arrangement of Emitter Molecules in Organic Light-Emitting Diode Films.

Tonnelé C, Stroet M, Caron B, Clulow AJ, Nagiri RCR, Malde AK, Burn PL, Gentle IR, Mark AE, Powell BJ.

Angew Chem Int Ed Engl. 2017 Jul 10;56(29):8402-8406. doi: 10.1002/anie.201610727. Epub 2017 Feb 7.


Deriving Structural Information from Experimentally Measured Data on Biomolecules.

van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ.

Angew Chem Int Ed Engl. 2016 Dec 23;55(52):15990-16010. doi: 10.1002/anie.201601828. Epub 2016 Nov 8. Review.


The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins.

Casey LW, Lavrencic P, Bentham AR, Cesari S, Ericsson DJ, Croll T, Turk D, Anderson PA, Mark AE, Dodds PN, Mobli M, Kobe B, Williams SJ.

Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):12856-12861. doi: 10.1073/pnas.1609922113. Epub 2016 Oct 17.


Revisiting the scissor-like mechanism of activation for the erythropoietin receptor.

Corbett MS, Poger D, Mark AE.

FEBS Lett. 2016 Sep;590(18):3083-8. doi: 10.1002/1873-3468.12340. Epub 2016 Aug 18. Review.


Interaction of Tarantula Venom Peptide ProTx-II with Lipid Membranes Is a Prerequisite for Its Inhibition of Human Voltage-gated Sodium Channel NaV1.7.

Henriques ST, Deplazes E, Lawrence N, Cheneval O, Chaousis S, Inserra M, Thongyoo P, King GF, Mark AE, Vetter I, Craik DJ, Schroeder CI.

J Biol Chem. 2016 Aug 12;291(33):17049-65. doi: 10.1074/jbc.M116.729095. Epub 2016 Jun 16.


Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.

Structure. 2016 Apr 5;24(4):502-508. doi: 10.1016/j.str.2016.02.017.


Validating lipid force fields against experimental data: Progress, challenges and perspectives.

Poger D, Caron B, Mark AE.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1556-65. doi: 10.1016/j.bbamem.2016.01.029. Epub 2016 Feb 3. Review.


Membrane-binding properties of gating modifier and pore-blocking toxins: Membrane interaction is not a prerequisite for modification of channel gating.

Deplazes E, Henriques ST, Smith JJ, King GF, Craik DJ, Mark AE, Schroeder CI.

Biochim Biophys Acta. 2016 Apr;1858(4):872-82. doi: 10.1016/j.bbamem.2016.02.002. Epub 2016 Feb 2.


Understanding the accumulation of P-glycoprotein substrates within cells: The effect of cholesterol on membrane partitioning.

Subramanian N, Schumann-Gillett A, Mark AE, O'Mara ML.

Biochim Biophys Acta. 2016 Apr;1858(4):776-82. doi: 10.1016/j.bbamem.2015.12.025. Epub 2015 Dec 23.


Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a.

Deplazes E, Davies J, Bonvin AM, King GF, Mark AE.

J Chem Inf Model. 2016 Jan 25;56(1):127-38. doi: 10.1021/acs.jcim.5b00529. Epub 2015 Dec 24.


Effect of Ring Size in ω-Alicyclic Fatty Acids on the Structural and Dynamical Properties Associated with Fluidity in Lipid Bilayers.

Poger D, Mark AE.

Langmuir. 2015 Oct 27;31(42):11574-82. doi: 10.1021/acs.langmuir.5b02635. Epub 2015 Oct 14.


A Comparison of Accelerometer Cut-Points among Individuals with Coronary Artery Disease.

Prince SA, Reed JL, Mark AE, Blanchard CM, Grace SL, Reid RD.

PLoS One. 2015 Sep 11;10(9):e0137759. doi: 10.1371/journal.pone.0137759. eCollection 2015.


Some Like It Hot: The Effect of Sterols and Hopanoids on Lipid Ordering at High Temperature.

Caron B, Mark AE, Poger D.

J Phys Chem Lett. 2014 Nov 20;5(22):3953-7. doi: 10.1021/jz5020778. Epub 2014 Nov 3.


Molecular dynamics and functional studies define a hot spot of crystal contacts essential for PcTx1 inhibition of acid-sensing ion channel 1a.

Saez NJ, Deplazes E, Cristofori-Armstrong B, Chassagnon IR, Lin X, Mobli M, Mark AE, Rash LD, King GF.

Br J Pharmacol. 2015 Oct;172(20):4985-95. doi: 10.1111/bph.13267. Epub 2015 Sep 22.


Binding of Starch Fragments to the Starch Branching Enzyme: Implications for Developing Slower-Digesting Starch.

Go RM, Mark AE, Malde AK, Gilbert RG.

Biomacromolecules. 2015 Aug 10;16(8):2475-81. doi: 10.1021/acs.biomac.5b00710. Epub 2015 Jul 9.


Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques.

Subramanian N, Condic-Jurkic K, Mark AE, O'Mara ML.

J Chem Inf Model. 2015 Jun 22;55(6):1202-17. doi: 10.1021/ci5007382. Epub 2015 May 18.


The characterization of modified starch branching enzymes: toward the control of starch chain-length distributions.

Li C, Wu AC, Go RM, Malouf J, Turner MS, Malde AK, Mark AE, Gilbert RG.

PLoS One. 2015 Apr 13;10(4):e0125507. doi: 10.1371/journal.pone.0125507. eCollection 2015.


A ring to rule them all: the effect of cyclopropane Fatty acids on the fluidity of lipid bilayers.

Poger D, Mark AE.

J Phys Chem B. 2015 Apr 30;119(17):5487-95. doi: 10.1021/acs.jpcb.5b00958. Epub 2015 Apr 16.


Effect of methyl-branched fatty acids on the structure of lipid bilayers.

Poger D, Caron B, Mark AE.

J Phys Chem B. 2014 Dec 4;118(48):13838-48. doi: 10.1021/jp503910r. Epub 2014 Nov 19.


Determining the structure of interfacial peptide films: comparing neutron reflectometry and molecular dynamics simulations.

Xue Y, He L, Middelberg AP, Mark AE, Poger D.

Langmuir. 2014 Aug 26;30(33):10080-9. doi: 10.1021/la501715h. Epub 2014 Aug 14.


Mechanism of activation of protein kinase JAK2 by the growth hormone receptor.

Brooks AJ, Dai W, O'Mara ML, Abankwa D, Chhabra Y, Pelekanos RA, Gardon O, Tunny KA, Blucher KM, Morton CJ, Parker MW, Sierecki E, Gambin Y, Gomez GA, Alexandrov K, Wilson IA, Doxastakis M, Mark AE, Waters MJ.

Science. 2014 May 16;344(6185):1249783. doi: 10.1126/science.1249783.


Does tautomerization of FapyG influence its mutagenicity?

Jena NR, Mark AE, Mishra PC.

Chemphyschem. 2014 Jun 23;15(9):1779-84. doi: 10.1002/cphc.201400045. Epub 2014 May 14.


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