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Items: 1 to 50 of 103

1.

Peppy: A virtual reality environment for exploring the principles of polypeptide structure.

Doak DG, Denyer GS, Gerrard JA, Mackay JP, Allison JR.

Protein Sci. 2019 Oct 17. doi: 10.1002/pro.3752. [Epub ahead of print]

PMID:
31622516
2.

Molecular Dynamics Simulation of Proteins.

Collier TA, Piggot TJ, Allison JR.

Methods Mol Biol. 2020;2073:311-327. doi: 10.1007/978-1-4939-9869-2_17.

PMID:
31612449
3.

Predicting orbital fractures in head injury: a preliminary study of clinical findings.

Allison JR, Kearns A, Banks RJ.

Emerg Radiol. 2019 Aug 30. doi: 10.1007/s10140-019-01720-0. [Epub ahead of print]

PMID:
31471701
4.

Brain Responses in CFS and TMD to Autonomic Challenges: An Exploratory fMRI Study.

Vuong QC, Allison JR, Finkelmeyer A, Newton J, Durham J.

JDR Clin Trans Res. 2019 Aug 28:2380084419872135. doi: 10.1177/2380084419872135. [Epub ahead of print]

PMID:
31461628
5.

CherryPicker: An Algorithm for the Automated Parametrization of Large Biomolecules for Molecular Simulation.

Welsh ID, Allison JR.

Front Chem. 2019 Jun 5;7:400. doi: 10.3389/fchem.2019.00400. eCollection 2019.

6.

Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions.

Huber RG, Carpenter TS, Dube N, Holdbrook DA, Ingólfsson HI, Irvine WA, Marzinek JK, Samsudin F, Allison JR, Khalid S, Bond PJ.

Methods Mol Biol. 2019;2003:1-30. doi: 10.1007/978-1-4939-9512-7_1.

PMID:
31218611
7.

Site-specific glycation of Aβ1-42 affects fibril formation and is neurotoxic.

Ng J, Kaur H, Collier T, Chang K, Brooks AES, Allison JR, Brimble MA, Hickey A, Birch NP.

J Biol Chem. 2019 May 31;294(22):8806-8818. doi: 10.1074/jbc.RA118.006846. Epub 2019 Apr 17.

PMID:
30996005
8.

Automated simultaneous assignment of bond orders and formal charges.

Welsh ID, Allison JR.

J Cheminform. 2019 Mar 6;11(1):18. doi: 10.1186/s13321-019-0340-0.

9.

Characterisation of N-(Octadecyl)-1,8-naphthalimide Monolayer Compression Using Molecular Dynamics and Experimental Approaches.

Welsh ID, Draper D, Kim J, Kitchen JA, Allison JR.

Chem Asian J. 2019 Apr 15;14(8):1221-1229. doi: 10.1002/asia.201801736. Epub 2019 Jan 21.

PMID:
30663846
10.

Infectious Disease: Health Care-Associated Infections.

Shafer CW, Allison JR, Hogue AL, Huntington MK.

FP Essent. 2019 Jan;476:30-42.

PMID:
30615408
11.

Infectious Disease: Community Response to Emerging Infectious Diseases.

Hogue AL, Allison JR, Shafer CW, Huntington MK.

FP Essent. 2019 Jan;476:25-29.

PMID:
30615407
12.

Infectious Disease: Bedbugs, Lice, and Mites.

Huntington MK, Allison JR, Hogue AL, Shafer CW.

FP Essent. 2019 Jan;476:18-24.

PMID:
30615406
13.

Infectious Disease: Mosquito-Borne Viral Illnesses.

Allison JR, Hogue AL, Shafer CW, Huntington MK.

FP Essent. 2019 Jan;476:11-17.

PMID:
30615405
14.

Computational Prediction of Amino Acids Governing Protein-Membrane Interaction for the PIP3 Cell Signaling System.

Irvine WA, Flanagan JU, Allison JR.

Structure. 2019 Feb 5;27(2):371-380.e3. doi: 10.1016/j.str.2018.10.014. Epub 2018 Dec 6.

PMID:
30528597
15.

The dispersion-brightness relation for fast radio bursts from a wide-field survey.

Shannon RM, Macquart JP, Bannister KW, Ekers RD, James CW, Osłowski S, Qiu H, Sammons M, Hotan AW, Voronkov MA, Beresford RJ, Brothers M, Brown AJ, Bunton JD, Chippendale AP, Haskins C, Leach M, Marquarding M, McConnell D, Pilawa MA, Sadler EM, Troup ER, Tuthill J, Whiting MT, Allison JR, Anderson CS, Bell ME, Collier JD, Gürkan G, Heald G, Riseley CJ.

Nature. 2018 Oct;562(7727):386-390. doi: 10.1038/s41586-018-0588-y. Epub 2018 Oct 10.

PMID:
30305732
16.

The Sodium Sialic Acid Symporter From Staphylococcus aureus Has Altered Substrate Specificity.

North RA, Wahlgren WY, Remus DM, Scalise M, Kessans SA, Dunevall E, Claesson E, Soares da Costa TP, Perugini MA, Ramaswamy S, Allison JR, Indiveri C, Friemann R, Dobson RCJ.

Front Chem. 2018 Jul 4;6:233. doi: 10.3389/fchem.2018.00233. eCollection 2018.

17.

The self-association and thermal denaturation of caprine and bovine β-lactoglobulin.

Crowther JM, Allison JR, Smolenski GA, Hodgkinson AJ, Jameson GB, Dobson RCJ.

Eur Biophys J. 2018 Oct;47(7):739-750. doi: 10.1007/s00249-018-1300-8. Epub 2018 Apr 16.

PMID:
29663020
18.

The Value of Cone Beam Computed Tomography in the Management of Dentigerous Cysts – A Review and Case Report.

Allison JR, Garlington G.

Dent Update. 2017 Mar;44(3):182-4, 186-8. Review.

PMID:
29172322
19.

Illuminating gravitational waves: A concordant picture of photons from a neutron star merger.

Kasliwal MM, Nakar E, Singer LP, Kaplan DL, Cook DO, Van Sistine A, Lau RM, Fremling C, Gottlieb O, Jencson JE, Adams SM, Feindt U, Hotokezaka K, Ghosh S, Perley DA, Yu PC, Piran T, Allison JR, Anupama GC, Balasubramanian A, Bannister KW, Bally J, Barnes J, Barway S, Bellm E, Bhalerao V, Bhattacharya D, Blagorodnova N, Bloom JS, Brady PR, Cannella C, Chatterjee D, Cenko SB, Cobb BE, Copperwheat C, Corsi A, De K, Dobie D, Emery SWK, Evans PA, Fox OD, Frail DA, Frohmaier C, Goobar A, Hallinan G, Harrison F, Helou G, Hinderer T, Ho AYQ, Horesh A, Ip WH, Itoh R, Kasen D, Kim H, Kuin NPM, Kupfer T, Lynch C, Madsen K, Mazzali PA, Miller AA, Mooley K, Murphy T, Ngeow CC, Nichols D, Nissanke S, Nugent P, Ofek EO, Qi H, Quimby RM, Rosswog S, Rusu F, Sadler EM, Schmidt P, Sollerman J, Steele I, Williamson AR, Xu Y, Yan L, Yatsu Y, Zhang C, Zhao W.

Science. 2017 Dec 22;358(6370):1559-1565. doi: 10.1126/science.aap9455. Epub 2017 Oct 16.

PMID:
29038373
20.

A radio counterpart to a neutron star merger.

Hallinan G, Corsi A, Mooley KP, Hotokezaka K, Nakar E, Kasliwal MM, Kaplan DL, Frail DA, Myers ST, Murphy T, De K, Dobie D, Allison JR, Bannister KW, Bhalerao V, Chandra P, Clarke TE, Giacintucci S, Ho AYQ, Horesh A, Kassim NE, Kulkarni SR, Lenc E, Lockman FJ, Lynch C, Nichols D, Nissanke S, Palliyaguru N, Peters WM, Piran T, Rana J, Sadler EM, Singer LP.

Science. 2017 Dec 22;358(6370):1579-1583. doi: 10.1126/science.aap9855. Epub 2017 Oct 16.

PMID:
29038372
21.

Direct Head-to-Head Evaluation of Recombinant Adeno-associated Viral Vectors Manufactured in Human versus Insect Cells.

Kondratov O, Marsic D, Crosson SM, Mendez-Gomez HR, Moskalenko O, Mietzsch M, Heilbronn R, Allison JR, Green KB, Agbandje-McKenna M, Zolotukhin S.

Mol Ther. 2017 Dec 6;25(12):2661-2675. doi: 10.1016/j.ymthe.2017.08.003. Epub 2017 Aug 10.

22.

On the Calculation of Acyl Chain Order Parameters from Lipid Simulations.

Piggot TJ, Allison JR, Sessions RB, Essex JW.

J Chem Theory Comput. 2017 Nov 14;13(11):5683-5696. doi: 10.1021/acs.jctc.7b00643. Epub 2017 Oct 16.

PMID:
28876925
23.

Block-restraining of residual dipolar couplings to allow fluctuating relative alignments of molecular subdomains.

Wirz LN, Allison JR.

Prog Biophys Mol Biol. 2017 Sep;128:133-141. doi: 10.1016/j.pbiomolbio.2017.02.006. Epub 2017 Feb 20.

PMID:
28223155
24.

Using simulation to interpret experimental data in terms of protein conformational ensembles.

Allison JR.

Curr Opin Struct Biol. 2017 Apr;43:79-87. doi: 10.1016/j.sbi.2016.11.018. Epub 2016 Dec 9. Review.

PMID:
27940377
25.

Molecular gas in the halo fuels the growth of a massive cluster galaxy at high redshift.

Emonts BH, Lehnert MD, Villar-Martín M, Norris RP, Ekers RD, van Moorsel GA, Dannerbauer H, Pentericci L, Miley GK, Allison JR, Sadler EM, Guillard P, Carilli CL, Mao MY, Röttgering HJ, De Breuck C, Seymour N, Gullberg B, Ceverino D, Jagannathan P, Vernet J, Indermuehle BT.

Science. 2016 Dec 2;354(6316):1128-1130.

PMID:
27934760
26.

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.

PMID:
27862777
27.

Molecular Dynamics Simulation of β-Lactoglobulin at Different Oil/Water Interfaces.

Zare D, Allison JR, McGrath KM.

Biomacromolecules. 2016 May 9;17(5):1572-81. doi: 10.1021/acs.biomac.5b01709. Epub 2016 Apr 25.

PMID:
27075297
28.

Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics.

Allison JR, Lechner M, Hoeppner MP, Poole AM.

PLoS One. 2016 Feb 12;11(2):e0147619. doi: 10.1371/journal.pone.0147619. eCollection 2016.

29.

Let the Powers Combine.

Allison JR.

Structure. 2016 Jan 5;24(1):5-6. doi: 10.1016/j.str.2015.12.003.

30.

A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe.

Pichugina T, Sugawara T, Kaykov A, Schierding W, Masuda K, Uewaki J, Grand RS, Allison JR, Martienssen RA, Nurse P, Ueno M, O'Sullivan JM.

Sci Rep. 2016 Jan 5;6:18757. doi: 10.1038/srep18757.

31.

Orthodontics: Treating avulsed permanent teeth.

Allison JR, Garlington G.

Br Dent J. 2015 Dec;219(11):514-5. doi: 10.1038/sj.bdj.2015.902. No abstract available.

PMID:
26657422
32.

Comment on "A Tensor-Free Method for the Structural and Dynamic Refinement of Proteins using Residual Dipolar Couplings".

Wirz LN, Allison JR.

J Phys Chem B. 2015 Jun 25;119(25):8223-4; discussion 8225-6. doi: 10.1021/acs.jpcb.5b02801. Epub 2015 Jun 15. No abstract available.

PMID:
26030336
33.

Deciphering β-Lactoglobulin Interactions at an Oil-Water Interface: A Molecular Dynamics Study.

Zare D, McGrath KM, Allison JR.

Biomacromolecules. 2015 Jun 8;16(6):1855-61. doi: 10.1021/acs.biomac.5b00467. Epub 2015 May 26.

PMID:
25989152
34.

Meta-analysis of porcine circovirus type 2 (PCV2) vaccines.

Allison JR, Nitzel GP, Taylor LP.

Prev Vet Med. 2015 Apr 1;119(1-2):93. doi: 10.1016/j.prevetmed.2015.01.012. Epub 2015 Jan 28. No abstract available.

PMID:
25697365
35.

Fitting alignment tensor components to experimental RDCs, CSAs and RQCs.

Wirz LN, Allison JR.

J Biomol NMR. 2015 May;62(1):25-9. doi: 10.1007/s10858-015-9907-x. Epub 2015 Feb 5.

PMID:
25652903
36.

A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein.

Allison JR, Rivers RC, Christodoulou JC, Vendruscolo M, Dobson CM.

Biochemistry. 2014 Nov 25;53(46):7170-83. doi: 10.1021/bi5009326. Epub 2014 Nov 12.

37.

Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure.

Grand RS, Pichugina T, Gehlen LR, Jones MB, Tsai P, Allison JR, Martienssen R, O'Sullivan JM.

Nucleic Acids Res. 2014 Nov 10;42(20):12585-99. doi: 10.1093/nar/gku965. Epub 2014 Oct 23.

38.

Optimum conditions for extracting collagen from the tunica albuginea of immunologically castrated pig testes and the functional properties of the isolated collagen.

Simões GS, Silveira ET, de Oliveira SR, Poleze E, Allison JR, Ida EI, Shimokomaki M.

Meat Sci. 2014 Apr;96(4):1460-8. doi: 10.1016/j.meatsci.2013.10.038. Epub 2013 Nov 8. Erratum in: Meat Sci. 2014 Aug;97(4):615.

PMID:
24412738
39.

The effect of immunization against GnRF on nutrient requirements of male pigs: a review.

Dunshea FR, Allison JR, Bertram M, Boler DD, Brossard L, Campbell R, Crane JP, Hennessy DP, Huber L, de Lange C, Ferguson N, Matzat P, McKeith F, Moraes PJ, Mullan BP, Noblet J, Quiniou N, Tokach M.

Animal. 2013 Nov;7(11):1769-78. doi: 10.1017/S1751731113001407. Epub 2013 Aug 9. Review.

PMID:
23931578
40.

Molecular dynamics simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data.

Smith LJ, Roby Y, Allison JR, van Gunsteren WF.

Biochemistry. 2013 Jul 30;52(30):5029-38. doi: 10.1021/bi4006573. Epub 2013 Jul 18.

PMID:
23834513
41.

Relative free enthalpies for point mutations in two proteins with highly similar sequences but different folds.

Hansen N, Allison JR, Hodel FH, van Gunsteren WF.

Biochemistry. 2013 Jul 23;52(29):4962-70. doi: 10.1021/bi400272q. Epub 2013 Jul 11.

PMID:
23802564
42.

Directed evolution of a model primordial enzyme provides insights into the development of the genetic code.

Müller MM, Allison JR, Hongdilokkul N, Gaillon L, Kast P, van Gunsteren WF, Marlière P, Hilvert D.

PLoS Genet. 2013;9(1):e1003187. doi: 10.1371/journal.pgen.1003187. Epub 2013 Jan 3.

43.

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.

Kleinjung J, Scott WR, Allison JR, van Gunsteren WF, Fraternali F.

J Chem Theory Comput. 2012 Jul 10;8(7):2391-2403. Epub 2012 Jun 12.

44.

Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12.

Smith LJ, Gunsteren WF, Allison JR.

Protein Sci. 2013 Jan;22(1):56-64. doi: 10.1002/pro.2184.

45.

Identifying multiple origins of polyploid taxa: a multilocus study of the hybrid cloak fern (Astrolepis integerrima; Pteridaceae).

Beck JB, Allison JR, Pryer KM, Windham MD.

Am J Bot. 2012 Nov;99(11):1857-65. doi: 10.3732/ajb.1200199. Epub 2012 Oct 29.

46.

Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data.

Allison JR, Hertig S, Missimer JH, Smith LJ, Steinmetz MO, Dolenc J.

J Chem Theory Comput. 2012 Oct 9;8(10):3430-44. doi: 10.1021/ct300393b. Epub 2012 Jul 30.

PMID:
26592994
47.

Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data.

Allison JR.

Biophys Rev. 2012 Sep;4(3):189-203. doi: 10.1007/s12551-012-0087-6. Epub 2012 Sep 1. Review.

48.

On the calculation of ³Jαβ-coupling constants for side chains in proteins.

Steiner D, Allison JR, Eichenberger AP, van Gunsteren WF.

J Biomol NMR. 2012 Jul;53(3):223-46. doi: 10.1007/s10858-012-9634-5. Epub 2012 Jun 20.

PMID:
22714630
49.

On developing coarse-grained models for biomolecular simulation: a review.

Riniker S, Allison JR, van Gunsteren WF.

Phys Chem Chem Phys. 2012 Sep 28;14(36):12423-30. doi: 10.1039/c2cp40934h. Epub 2012 Jun 8. Review.

PMID:
22678152
50.

Arterial sampler filling time during arterial and venous punctures, and its relationship with mean arterial pressure in human subjects.

Bender JJ, Allison JR, Goehring JJ, Patel MD, Niederst SM, Douce FH.

Respir Care. 2012 Nov;57(11):1945-8. doi: 10.4187/respcare.01713. Epub 2012 May 14.

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