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Items: 50

1.

Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator.

Xiong Y, Onufriev AV.

PLoS One. 2019 Nov 14;14(11):e0224991. doi: 10.1371/journal.pone.0224991. eCollection 2019.

2.

General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins.

Shabane PS, Izadi S, Onufriev AV.

J Chem Theory Comput. 2019 Apr 9;15(4):2620-2634. doi: 10.1021/acs.jctc.8b01123. Epub 2019 Mar 26.

PMID:
30865832
3.

Generalized Born Implicit Solvent Models for Biomolecules.

Onufriev AV, Case DA.

Annu Rev Biophys. 2019 May 6;48:275-296. doi: 10.1146/annurev-biophys-052118-115325. Epub 2019 Mar 11.

4.

The nucleosome: from structure to function through physics.

Onufriev AV, Schiessel H.

Curr Opin Struct Biol. 2019 Jun;56:119-130. doi: 10.1016/j.sbi.2018.11.003. Epub 2019 Jan 30. Review.

PMID:
30710748
5.

Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.

Anandakrishnan R, Izadi S, Onufriev AV.

J Chem Theory Comput. 2019 Jan 8;15(1):625-636. doi: 10.1021/acs.jctc.8b00485. Epub 2018 Dec 20.

PMID:
30514080
6.

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.

7.

The Role of Chromosome-Nuclear Envelope Attachments in 3D Genome Organization.

Sharakhov IV, Bondarenko SM, Artemov GN, Onufriev AV.

Biochemistry (Mosc). 2018 Apr;83(4):350-358. doi: 10.1134/S0006297918040065. Review.

8.

Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core.

Fenley AT, Anandakrishnan R, Kidane YH, Onufriev AV.

Epigenetics Chromatin. 2018 Mar 16;11(1):11. doi: 10.1186/s13072-018-0181-5.

9.

Linear relationship between peak and season-long abundances in insects.

Onufrieva KS, Onufriev AV.

PLoS One. 2018 Feb 22;13(2):e0193110. doi: 10.1371/journal.pone.0193110. eCollection 2018.

10.

Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.

Izadi S, Harris RC, Fenley MO, Onufriev AV.

J Chem Theory Comput. 2018 Mar 13;14(3):1656-1670. doi: 10.1021/acs.jctc.7b00886. Epub 2018 Feb 15.

PMID:
29378399
11.

Chromosome-nuclear envelope attachments affect interphase chromosome territories and entanglement.

Kinney NA, Sharakhov IV, Onufriev AV.

Epigenetics Chromatin. 2018 Jan 22;11(1):3. doi: 10.1186/s13072-018-0173-5.

12.

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.

Forouzesh N, Izadi S, Onufriev AV.

J Chem Inf Model. 2017 Oct 23;57(10):2505-2513. doi: 10.1021/acs.jcim.7b00192. Epub 2017 Oct 5.

PMID:
28786669
13.

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.

14.

Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

Katkova EV, Onufriev AV, Aguilar B, Sulimov VB.

J Mol Graph Model. 2017 Mar;72:70-80. doi: 10.1016/j.jmgm.2016.12.011. Epub 2016 Dec 21.

15.

Partially Assembled Nucleosome Structures at Atomic Detail.

Rychkov GN, Ilatovskiy AV, Nazarov IB, Shvetsov AV, Lebedev DV, Konev AY, Isaev-Ivanov VV, Onufriev AV.

Biophys J. 2017 Feb 7;112(3):460-472. doi: 10.1016/j.bpj.2016.10.041. Epub 2016 Dec 28.

16.

Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.

Izadi S, Anandakrishnan R, Onufriev AV.

J Chem Theory Comput. 2016 Dec 13;12(12):5946-5959. Epub 2016 Nov 7.

17.

Accuracy limit of rigid 3-point water models.

Izadi S, Onufriev AV.

J Chem Phys. 2016 Aug 21;145(7):074501. doi: 10.1063/1.4960175.

18.

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.

19.

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.

20.

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.

21.

The Role of Correlation and Solvation in Ion Interactions with B-DNA.

Sushko ML, Thomas DG, Pabit SA, Pollack L, Onufriev AV, Baker NA.

Biophys J. 2016 Jan 19;110(2):315-326. doi: 10.1016/j.bpj.2015.12.011.

22.

Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.

Izadi S, Aguilar B, Onufriev AV.

J Chem Theory Comput. 2015 Sep 8;11(9):4450-9. doi: 10.1021/acs.jctc.5b00483. Epub 2015 Aug 21.

23.

Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes.

Kinney NA, Onufriev AV, Sharakhov IV.

Nucleus. 2015;6(3):212-24. doi: 10.1080/19491034.2015.1056441.

24.

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
25.

Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.

Anandakrishnan R, Drozdetski A, Walker RC, Onufriev AV.

Biophys J. 2015 Mar 10;108(5):1153-64. doi: 10.1016/j.bpj.2014.12.047.

26.

Building Water Models: A Different Approach.

Izadi S, Anandakrishnan R, Onufriev AV.

J Phys Chem Lett. 2014 Nov 6;5(21):3863-3871. Epub 2014 Oct 16.

27.

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.

28.

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.

29.
30.

Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach.

Kinney NA, Sharakhov IV, Onufriev AV.

PLoS One. 2014 Mar 20;9(3):e91943. doi: 10.1371/journal.pone.0091943. eCollection 2014.

31.

Protonation and pK changes in protein-ligand binding.

Onufriev AV, Alexov E.

Q Rev Biophys. 2013 May;46(2):181-209. doi: 10.1017/S0033583513000024. Review.

32.

Point charges optimally placed to represent the multipole expansion of charge distributions.

Anandakrishnan R, Baker C, Izadi S, Onufriev AV.

PLoS One. 2013 Jul 4;8(7):e67715. doi: 10.1371/journal.pone.0067715. Print 2013.

33.

Two-phase stretching of molecular chains.

Savin AV, Kikot IP, Mazo MA, Onufriev AV.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2816-21. doi: 10.1073/pnas.1218677110. Epub 2013 Feb 1.

34.

Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model.

Aguilar B, Onufriev AV.

J Chem Theory Comput. 2012 Jul 10;8(7):2404-11. doi: 10.1021/ct200786m. Epub 2012 Jun 8.

PMID:
26588972
35.

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.

36.

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

Anandakrishnan R, Aguilar B, Onufriev AV.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W537-41. doi: 10.1093/nar/gks375. Epub 2012 May 8.

37.

[New coarse-grained DNA model].

Kikot' IP, Savin AV, Zubova EA, Mzo MA, Gusarova EB, Manevich LI, Onufriev AV.

Biofizika. 2011 May-Jun;56(3):396-402. Russian.

PMID:
21786691
38.

Heat conductivity of DNA double helix.

Savin AV, Mazo MA, Kikot IP, Manevitch LI, Onufriev AV.

Phys Rev B Condens Matter Mater Phys. 2011 Jun 15;83(24). pii: 245406.

39.

A strategy for reducing gross errors in the generalized Born models of implicit solvation.

Onufriev AV, Sigalov G.

J Chem Phys. 2011 Apr 28;134(16):164104. doi: 10.1063/1.3578686.

40.

An n log n Generalized Born Approximation.

Anandakrishnan R, Daga M, Onufriev AV.

J Chem Theory Comput. 2011 Mar 8;7(3):544-59. doi: 10.1021/ct100390b. Epub 2011 Jan 27.

PMID:
26596289
41.

Charge state of the globular histone core controls stability of the nucleosome.

Fenley AT, Adams DA, Onufriev AV.

Biophys J. 2010 Sep 8;99(5):1577-85. doi: 10.1016/j.bpj.2010.06.046.

42.

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units.

Anandakrishnan R, Scogland TR, Fenley AT, Gordon JC, Feng WC, Onufriev AV.

J Mol Graph Model. 2010 Jun;28(8):904-10. doi: 10.1016/j.jmgm.2010.04.001.

43.

Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations.

Palpant NJ, Houang EM, Delport W, Hastings KE, Onufriev AV, Sham YY, Metzger JM.

Physiol Genomics. 2010 Jul 7;42(2):287-99. doi: 10.1152/physiolgenomics.00033.2010. Epub 2010 Apr 27.

44.

Statistics and physical origins of pK and ionization state changes upon protein-ligand binding.

Aguilar B, Anandakrishnan R, Ruscio JZ, Onufriev AV.

Biophys J. 2010 Mar 3;98(5):872-80. doi: 10.1016/j.bpj.2009.11.016.

45.
46.

Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin.

Ruscio JZ, Kumar D, Shukla M, Prisant MG, Murali TM, Onufriev AV.

Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9204-9. doi: 10.1073/pnas.0710825105. Epub 2008 Jul 1.

47.

Modeling of flap endonuclease interactions with DNA substrate.

Allawi HT, Kaiser MW, Onufriev AV, Ma WP, Brogaard AE, Case DA, Neri BP, Lyamichev VI.

J Mol Biol. 2003 May 2;328(3):537-54.

PMID:
12706715
48.

Theoretical studies of time-resolved spectroscopy of protein folding.

Hirst JD, Bhattacharjee S, Onufriev AV.

Faraday Discuss. 2003;122:253-67; discussion 269-82.

PMID:
12555862
49.

Memory loss and Auger processes in a many-body theory of charge transfer.

Onufriev AV, Marston JB.

Phys Rev B Condens Matter. 1996 May 15;53(20):13340-13356. No abstract available.

PMID:
9983078
50.

[Evaluation of the immune status in cattle herds with foot-and-mouth disease].

Murav'ev VK, Maliarets PV, Onufriev AV, Shorshnev VI, Sorokin VA.

Veterinariia. 1979 May;(5):31-4. Russian. No abstract available.

PMID:
452388

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