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Items: 29

1.

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows.

Yang PC, Purawat S, Ieong PU, Jeng MT, DeMarco KR, Vorobyov I, McCulloch AD, Altintas I, Amaro RE, Clancy CE.

PLoS Comput Biol. 2019 Mar 8;15(3):e1006856. doi: 10.1371/journal.pcbi.1006856. eCollection 2019 Mar.

2.

Structural basis for antiarrhythmic drug interactions with the human cardiac sodium channel.

Nguyen PT, DeMarco KR, Vorobyov I, Clancy CE, Yarov-Yarovoy V.

Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):2945-2954. doi: 10.1073/pnas.1817446116. Epub 2019 Feb 6.

3.

Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation.

DeMarco KR, Bekker S, Vorobyov I.

J Physiol. 2019 Feb;597(3):679-698. doi: 10.1113/JP277088. Epub 2018 Dec 19.

PMID:
30471114
4.

Exploring the free-energy landscape of GPCR activation.

Alhadeff R, Vorobyov I, Yoon HW, Warshel A.

Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):10327-10332. doi: 10.1073/pnas.1810316115. Epub 2018 Sep 26.

5.

Sex, drugs, and funky rhythms.

Vorobyov I, Clancy CE.

Heart Rhythm. 2018 Apr;15(4):485-486. doi: 10.1016/j.hrthm.2018.01.028. No abstract available.

PMID:
29605014
6.

Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations.

DeMarco KR, Bekker S, Clancy CE, Noskov SY, Vorobyov I.

Front Pharmacol. 2018 Feb 1;9:26. doi: 10.3389/fphar.2018.00026. eCollection 2018.

7.

A multiscale computational modelling approach predicts mechanisms of female sex risk in the setting of arousal-induced arrhythmias.

Yang PC, Perissinotti LL, López-Redondo F, Wang Y, DeMarco KR, Jeng MT, Vorobyov I, Harvey RD, Kurokawa J, Noskov SY, Clancy CE.

J Physiol. 2017 Jul 15;595(14):4695-4723. doi: 10.1113/JP273142. Epub 2017 Jun 14.

8.

Refining the treatment of membrane proteins by coarse-grained models.

Vorobyov I, Kim I, Chu ZT, Warshel A.

Proteins. 2016 Jan;84(1):92-117. doi: 10.1002/prot.24958. Epub 2015 Dec 9.

9.

Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel.

Boiteux C, Vorobyov I, French RJ, French C, Yarov-Yarovoy V, Allen TW.

Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13057-62. doi: 10.1073/pnas.1408710111. Epub 2014 Aug 18.

10.

Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel.

Boiteux C, Vorobyov I, Allen TW.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3454-9. doi: 10.1073/pnas.1320907111. Epub 2014 Feb 18.

11.

Ion-induced defect permeation of lipid membranes.

Vorobyov I, Olson TE, Kim JH, Koeppe RE 2nd, Andersen OS, Allen TW.

Biophys J. 2014 Feb 4;106(3):586-97. doi: 10.1016/j.bpj.2013.12.027.

12.

The different interactions of lysine and arginine side chains with lipid membranes.

Li L, Vorobyov I, Allen TW.

J Phys Chem B. 2013 Oct 10;117(40):11906-20. doi: 10.1021/jp405418y. Epub 2013 Sep 27.

13.

The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers.

Vorobyov I, Bennett WF, Tieleman DP, Allen TW, Noskov S.

J Chem Theory Comput. 2012 Feb 14;8(2):618-28. doi: 10.1021/ct200417p. Epub 2012 Jan 18.

PMID:
26596610
14.

The role of membrane thickness in charged protein-lipid interactions.

Li LB, Vorobyov I, Allen TW.

Biochim Biophys Acta. 2012 Feb;1818(2):135-45. doi: 10.1016/j.bbamem.2011.10.026. Epub 2011 Oct 28.

15.

On the role of anionic lipids in charged protein interactions with membranes.

Vorobyov I, Allen TW.

Biochim Biophys Acta. 2011 Jun;1808(6):1673-83. doi: 10.1016/j.bbamem.2010.11.009. Epub 2010 Nov 10.

16.

Electrostatics of deformable lipid membranes.

Vorobyov I, Bekker B, Allen TW.

Biophys J. 2010 Jun 16;98(12):2904-13. doi: 10.1016/j.bpj.2010.03.046.

17.

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD Jr, Pastor RW.

J Phys Chem B. 2010 Jun 17;114(23):7830-43. doi: 10.1021/jp101759q.

18.

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, Mackerell AD Jr, Roux B.

J Chem Theory Comput. 2010;6(3):774-786.

19.

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr.

J Comput Chem. 2010 Mar;31(4):671-90. doi: 10.1002/jcc.21367.

20.

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

Anisimov VM, Vorobyov IV, Roux B, Mackerell AD Jr.

J Chem Theory Comput. 2007;3(6):1927-1946.

21.

Potential of mean force and pKa profile calculation for a lipid membrane-exposed arginine side chain.

Li L, Vorobyov I, Allen TW.

J Phys Chem B. 2008 Aug 14;112(32):9574-87. doi: 10.1021/jp7114912. Epub 2008 Jul 18.

PMID:
18636765
22.

Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane.

Vorobyov I, Li L, Allen TW.

J Phys Chem B. 2008 Aug 14;112(32):9588-602. doi: 10.1021/jp711492h. Epub 2008 Jul 18.

PMID:
18636764
23.

Is arginine charged in a membrane?

Li L, Vorobyov I, MacKerell AD Jr, Allen TW.

Biophys J. 2008 Jan 15;94(2):L11-3. Epub 2007 Nov 2.

24.

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

Vorobyov I, Anisimov VM, Greene S, Venable RM, Moser A, Pastor RW, MacKerell AD.

J Chem Theory Comput. 2007 May;3(3):1120-33. doi: 10.1021/ct600350s.

PMID:
26627431
25.

Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator.

Harder E, Anisimov VM, Vorobyov IV, Lopes PE, Noskov SY, MacKerell AD, Roux B.

J Chem Theory Comput. 2006 Nov;2(6):1587-97. doi: 10.1021/ct600180x.

PMID:
26627029
26.

Polarizable empirical force field for alkanes based on the classical Drude oscillator model.

Vorobyov IV, Anisimov VM, MacKerell AD Jr.

J Phys Chem B. 2005 Oct 13;109(40):18988-99.

PMID:
16853445
27.

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator.

Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD.

J Chem Theory Comput. 2005 Jan;1(1):153-68. doi: 10.1021/ct049930p.

PMID:
26641126
28.

Glycero- versus sphingo-phospholipids: correlations with human and non-human mammalian lens growth.

Yappert MC, Rujoi M, Borchman D, Vorobyov I, Estrada R.

Exp Eye Res. 2003 Jun;76(6):725-34.

PMID:
12742355
29.

Conformational studies of sphingolipids by NMR spectroscopy. II. Sphingomyelin.

Talbott CM, Vorobyov I, Borchman D, Taylor KG, DuPré DB, Yappert MC.

Biochim Biophys Acta. 2000 Aug 25;1467(2):326-37.

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