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Items: 1 to 20 of 57

1.

Snails In Silico: A Review of Computational Studies on the Conopeptides.

Mansbach RA, Travers T, McMahon BH, Fair JM, Gnanakaran S.

Mar Drugs. 2019 Mar 1;17(3). pii: E145. doi: 10.3390/md17030145. Review.

2.

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design.

Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B.

Cell Host Microbe. 2019 Jan 9;25(1):59-72.e8. doi: 10.1016/j.chom.2018.12.001.

3.

Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans.

López CA, Unkefer CJ, Swanson BI, Swanson JMJ, Gnanakaran S.

PLoS Comput Biol. 2018 Feb 5;14(2):e1005972. doi: 10.1371/journal.pcbi.1005972. eCollection 2018 Feb.

4.

Switch Loop Flexibility Affects Substrate Transport of the AcrB Efflux Pump.

Müller RT, Travers T, Cha HJ, Phillips JL, Gnanakaran S, Pos KM.

J Mol Biol. 2017 Dec 8;429(24):3863-3874. doi: 10.1016/j.jmb.2017.09.018. Epub 2017 Oct 5.

PMID:
28987732
5.

Broadly targeted CD8⁺ T cell responses restricted by major histocompatibility complex E.

Hansen SG, Wu HL, Burwitz BJ, Hughes CM, Hammond KB, Ventura AB, Reed JS, Gilbride RM, Ainslie E, Morrow DW, Ford JC, Selseth AN, Pathak R, Malouli D, Legasse AW, Axthelm MK, Nelson JA, Gillespie GM, Walters LC, Brackenridge S, Sharpe HR, López CA, Früh K, Korber BT, McMichael AJ, Gnanakaran S, Sacha JB, Picker LJ.

Science. 2016 Feb 12;351(6274):714-20. doi: 10.1126/science.aac9475. Epub 2016 Jan 21.

6.

Membrane-mediated regulation of the intrinsically disordered CD3ϵ cytoplasmic tail of the TCR.

López CA, Sethi A, Goldstein B, Wilson BS, Gnanakaran S.

Biophys J. 2015 May 19;108(10):2481-2491. doi: 10.1016/j.bpj.2015.03.059.

7.

MARTINI coarse-grained model for crystalline cellulose microfibers.

López CA, Bellesia G, Redondo A, Langan P, Chundawat SP, Dale BE, Marrink SJ, Gnanakaran S.

J Phys Chem B. 2015 Jan 15;119(2):465-73. doi: 10.1021/jp5105938. Epub 2015 Jan 6.

PMID:
25417548
8.

Improving pandemic influenza risk assessment.

Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, Macken CA, Maurer-Stroh S, Neuhaus E, Parrish CR, Pepin KM, Shepard SS, Smith DL, Suarez DL, Trock SC, Widdowson MA, George DB, Lipsitch M, Bloom JD.

Elife. 2014 Oct 16;3:e03883. doi: 10.7554/eLife.03883.

9.

The Seventh q-bio Conference: meeting report and preface.

Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y.

Phys Biol. 2014 Aug;11(4):040301. doi: 10.1088/1478-3975/11/4/040301. Epub 2014 Jul 30. No abstract available.

10.

A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps.

Phillips JL, Gnanakaran S.

Proteins. 2015 Jan;83(1):46-65. doi: 10.1002/prot.24632. Epub 2014 Nov 18.

PMID:
24957790
11.

Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment.

Mayes HB, Tian J, Nolte MW, Shanks BH, Beckham GT, Gnanakaran S, Broadbelt LJ.

J Phys Chem B. 2014 Feb 27;118(8):1990-2000. doi: 10.1021/jp409481f. Epub 2013 Dec 17.

PMID:
24308866
12.

Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial.

Gottardo R, Bailer RT, Korber BT, Gnanakaran S, Phillips J, Shen X, Tomaras GD, Turk E, Imholte G, Eckler L, Wenschuh H, Zerweck J, Greene K, Gao H, Berman PW, Francis D, Sinangil F, Lee C, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, Robb ML, Michael NL, Kim JH, Zolla-Pazner S, Haynes BF, Mascola JR, Self S, Gilbert P, Montefiori DC.

PLoS One. 2013 Sep 26;8(9):e75665. doi: 10.1371/journal.pone.0075665. eCollection 2013.

13.

Binding and movement of individual Cel7A cellobiohydrolases on crystalline cellulose surfaces revealed by single-molecule fluorescence imaging.

Jung J, Sethi A, Gaiotto T, Han JJ, Jeoh T, Gnanakaran S, Goodwin PM.

J Biol Chem. 2013 Aug 16;288(33):24164-72. doi: 10.1074/jbc.M113.455758. Epub 2013 Jul 1.

14.

Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis.

Gao D, Chundawat SP, Sethi A, Balan V, Gnanakaran S, Dale BE.

Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):10922-7. doi: 10.1073/pnas.1213426110. Epub 2013 Jun 19.

15.

Special section dedicated to The Sixth q-bio Conference: meeting report and preface.

Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR.

Phys Biol. 2013 Jun;10(3):030301. doi: 10.1088/1478-3975/10/3/030301. Epub 2013 Jun 4. No abstract available.

PMID:
23735417
16.

A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein.

Sethi A, Tian J, Derdeyn CA, Korber B, Gnanakaran S.

PLoS Comput Biol. 2013;9(5):e1003046. doi: 10.1371/journal.pcbi.1003046. Epub 2013 May 16.

17.

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.

Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L; NISC Comparative Sequencing Program, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF.

Nature. 2013 Apr 25;496(7446):469-76. doi: 10.1038/nature12053. Epub 2013 Apr 3.

18.

Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth.

Murphy MK, Yue L, Pan R, Boliar S, Sethi A, Tian J, Pfafferot K, Karita E, Allen SA, Cormier E, Goepfert PA, Borrow P, Robinson JE, Gnanakaran S, Hunter E, Kong XP, Derdeyn CA.

PLoS Pathog. 2013 Feb;9(2):e1003173. doi: 10.1371/journal.ppat.1003173. Epub 2013 Feb 28.

19.

Taste of sugar at the membrane: thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers.

Tian J, Sethi A, Swanson BI, Goldstein B, Gnanakaran S.

Biophys J. 2013 Feb 5;104(3):622-32. doi: 10.1016/j.bpj.2012.12.011.

20.

Identification of minimally interacting modules in an intrinsically disordered protein.

Sethi A, Tian J, Vu DM, Gnanakaran S.

Biophys J. 2012 Aug 22;103(4):748-57. doi: 10.1016/j.bpj.2012.06.052.

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