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Items: 20

1.

Explicit ions/implicit water generalized Born model for nucleic acids.

Tolokh IS, Thomas DG, Onufriev AV.

J Chem Phys. 2018 May 21;148(19):195101. doi: 10.1063/1.5027260.

PMID:
30307229
2.

Spermine Condenses DNA, but Not RNA Duplexes.

Katz AM, Tolokh IS, Pabit SA, Baker N, Onufriev AV, Pollack L.

Biophys J. 2017 Jan 10;112(1):22-30. doi: 10.1016/j.bpj.2016.11.018.

3.

Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA.

Drozdetski AV, Tolokh IS, Pollack L, Baker N, Onufriev AV.

Phys Rev Lett. 2016 Jul 8;117(2):028101. doi: 10.1103/PhysRevLett.117.028101. Epub 2016 Jul 6.

4.

Multi-shell model of ion-induced nucleic acid condensation.

Tolokh IS, Drozdetski AV, Pollack L, Baker NA, Onufriev AV.

J Chem Phys. 2016 Apr 21;144(15):155101. doi: 10.1063/1.4945382.

5.

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations.

Pabit SA, Katz AM, Tolokh IS, Drozdetski A, Baker N, Onufriev AV, Pollack L.

J Chem Phys. 2016 May 28;144(20):205102. doi: 10.1063/1.4950814.

6.

A Case of Diabetic Ketoacidosis Following Chikungunya Virus Infection.

Tolokh I, Laux T, Kim D.

Am J Trop Med Hyg. 2015 Aug;93(2):401-3. doi: 10.4269/ajtmh.14-0840. Epub 2015 Jun 1.

7.

Accurate evaluation of charge asymmetry in aqueous solvation.

Mukhopadhyay A, Tolokh IS, Onufriev AV.

J Phys Chem B. 2015 May 21;119(20):6092-100. doi: 10.1021/acs.jpcb.5b00602. Epub 2015 May 7.

PMID:
25830623
8.

Why double-stranded RNA resists condensation.

Tolokh IS, Pabit SA, Katz AM, Chen Y, Drozdetski A, Baker N, Pollack L, Onufriev AV.

Nucleic Acids Res. 2014;42(16):10823-31. doi: 10.1093/nar/gku756. Epub 2014 Aug 14.

9.

Introducing Charge Hydration Asymmetry into the Generalized Born Model.

Mukhopadhyay A, Aguilar BH, Tolokh IS, Onufriev AV.

J Chem Theory Comput. 2014 Apr 8;10(4):1788-1794. Epub 2014 Feb 18.

10.

Reliable sex and strain discrimination in the mouse vomeronasal organ and accessory olfactory bulb.

Tolokh II, Fu X, Holy TE.

J Neurosci. 2013 Aug 21;33(34):13903-13. doi: 10.1523/JNEUROSCI.0037-13.2013.

11.

Charge hydration asymmetry: the basic principle and how to use it to test and improve water models.

Mukhopadhyay A, Fenley AT, Tolokh IS, Onufriev AV.

J Phys Chem B. 2012 Aug 16;116(32):9776-83. doi: 10.1021/jp305226j. Epub 2012 Aug 7.

12.

Binding free energy and counterion release for adsorption of the antimicrobial peptide lactoferricin B on a POPG membrane.

Tolokh IS, Vivcharuk V, Tomberli B, Gray CG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Sep;80(3 Pt 1):031911. Epub 2009 Sep 22.

PMID:
19905150
13.

Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane.

Vivcharuk V, Tomberli B, Tolokh IS, Gray CG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Mar;77(3 Pt 1):031913. Epub 2008 Mar 14.

PMID:
18517428
14.

Nonequilibrium molecular dynamics calculation of the conductance of the KcsA potassium ion channel.

de Haan HW, Tolokh IS, Gray CG, Goldman S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Sep;74(3 Pt 1):030905. Epub 2006 Sep 26.

PMID:
17025587
15.

Unified modeling of conductance kinetics for low- and high-conductance potassium ion channels.

Tolokh IS, Goldman S, Gray CG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jul;74(1 Pt 1):011902. Epub 2006 Jul 5.

PMID:
16907122
16.

Conduction through the inward rectifier potassium channel, Kir2.1, is increased by negatively charged extracellular residues.

D'Avanzo N, Cho HC, Tolokh I, Pekhletski R, Tolokh I, Gray C, Goldman S, Backx PH.

J Gen Physiol. 2005 May;125(5):493-503. Epub 2005 Apr 11.

17.

Non-Michaelis-Menten kinetics model for conductance of low-conductance potassium ion channels.

Tolokh IS, Tolokh II, Cho HC, D'Avanzo N, Backx PH, Goldman S, Gray CG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Feb;71(2 Pt 1):021912. Epub 2005 Feb 24.

PMID:
15783357
18.

Hydration of uracil and thymine methylderivatives: a Monte Carlo simulation.

Danilov VI, Tolokh IS.

J Biomol Struct Dyn. 1990 Apr;7(5):1167-83.

PMID:
2361005
19.

Nature of the stacking of nucleic acid bases in water: a Monte Carlo simulation.

Danilov VI, Tolokh IS.

J Biomol Struct Dyn. 1984 Aug;2(1):119-30.

PMID:
6400926
20.

[Nature of the stacking interactions of nucleic acid bases in water: a study using the Monte Carlo method].

Danilov VI, Tolokh IS.

Dokl Akad Nauk SSSR. 1984;274(4):968-72. Russian. No abstract available.

PMID:
6734411

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