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Igor V. Vorobyov, Ph.D. - Publications

Affiliations: 
2003 University of Louisville, Louisville, KY, United States 
Area:
Physical Chemistry, General Biophysics
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49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Chen P, Vorobyov I, Roux B, Allen TW. Molecular Dynamics Simulations Based on Polarizable Models Show that Ion Permeation Interconverts between Different Mechanisms as a Function of Membrane Thickness. The Journal of Physical Chemistry. B. PMID 33493394 DOI: 10.1021/acs.jpcb.0c08613  0.304
2020 Yang PC, DeMarco KR, Aghasafari P, Jeng MT, Dawson JR, Bekker S, Noskov S, Yarov-Yarovoy V, Vorobyov I, Clancy CE. A Computational Pipeline to Predict Cardiotoxicity:From the Atom to the Rhythm. Circulation Research. PMID 32091972 DOI: 10.1161/Circresaha.119.316404  0.347
2020 Miranda WE, DeMarco KR, Guo J, Duff HJ, Vorobyov I, Clancy CE, Noskov SY. Selectivity filter modalities and rapid inactivation of the hERG1 channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 31980532 DOI: 10.1073/Pnas.1909196117  0.352
2020 Maly J, Emigh AM, DeMarco K, Sack JT, Vorobyov IV, Clancy CE, Yarov-Yarovoy V. Structural Modeling of the hERG Channel in an Inactivated State and Associated Drug Interactions Biophysical Journal. 118: 212a. DOI: 10.1016/J.Bpj.2019.11.1265  0.372
2019 Flood E, Boiteux C, Lev B, Vorobyov I, Allen TW. Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. Chemical Reviews. PMID 31246417 DOI: 10.1021/Acs.Chemrev.8B00630  0.415
2019 Nguyen PT, DeMarco KR, Vorobyov I, Clancy CE, Yarov-Yarovoy V. Structural basis for antiarrhythmic drug interactions with the human cardiac sodium channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 30728299 DOI: 10.1073/Pnas.1817446116  0.37
2019 DeMarco KR, Bekker S, Vorobyov I. Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation. The Journal of Physiology. 597: 679-698. PMID 30471114 DOI: 10.1113/Jp277088  0.382
2019 Dawson JR, DeMarco KR, Bekker B, Noskov SY, Clancy CE, Vorobyov IV. In Silico Determination of Open Conducting and Inactivated Atomistic KV11.1 Channel Models Biophysical Journal. 116: 103a. DOI: 10.1016/J.Bpj.2018.11.591  0.325
2019 Emigh AM, DeMarco KR, Furutani K, Sack JT, Clancy CE, Vorobyov IV, Yarov-Yarovoy V. Structural Modeling of Drug Interactions with hERG Channel in Open and Closed States Biophysical Journal. 116: 249a-250a. DOI: 10.1016/J.Bpj.2018.11.1363  0.373
2018 DeMarco KR, Bekker S, Clancy CE, Noskov SY, Vorobyov I. Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations. Frontiers in Pharmacology. 9: 26. PMID 29449809 DOI: 10.3389/Fphar.2018.00026  0.435
2018 Vorobyov I, Brown BM, DeMarco KR, Noskov SY, Yarov-Yarovoy V, Wulff H, Clancy CE. Molecular Determinants of Steroid Hormone and Drug Induced Arrhythmogenesis via hERG Channel Block Biophysical Journal. 114: 486a. DOI: 10.1016/J.Bpj.2017.11.2670  0.328
2018 Emigh AM, DeMarco KR, Furutani K, Bekker S, Sack JT, Clancy CE, Vorobyov I, Yarov-Yarovoy V. Structural Modeling of hERG Channel Interactions with Drugs using Rosetta Biophysical Journal. 114: 486a. DOI: 10.1016/J.Bpj.2017.11.2667  0.366
2018 Nguyen PT, DeMarco KR, Vorobyov I, Clancy CE, Yarov-Yarovoy V. Structural Modeling of Local Anesthetic and Antiarrhythmic Drug Binding to the Human Cardiac Voltage Gated Sodium Channel Biophysical Journal. 114: 39a. DOI: 10.1016/J.Bpj.2017.11.263  0.327
2018 DeMarco KR, Bekker S, Clancy CE, Noskov SY, Vorobyov I. Atomistic Simulation of Lipid Membrane Permeation for Cardiac Ion Channel Blockers Biophysical Journal. 114: 310a. DOI: 10.1016/J.Bpj.2017.11.1755  0.385
2017 Nguyen PT, DeMarco KR, Vorobyov I, Clancy CE, Allen TW, Yarov-Yarovoy V. An Open State Model of the Navab Channel Explored by Rosetta and Molecular Dynamics Simulation Biophysical Journal. 112: 105a. DOI: 10.1016/J.Bpj.2016.11.599  0.393
2017 DeMarco KR, Nguyen PT, Allen TW, Yarov-Yarovoy V, Clancy CE, Vorobyov I. State-Dependent Structural Modeling and Atomistic Simulations of the hERG Potassium Channel Biophysical Journal. 112: 542a. DOI: 10.1016/J.Bpj.2016.11.2929  0.355
2015 Vorobyov I, Kim I, Chu ZT, Warshel A. Refining the treatment of membrane proteins by coarse-grained models. Proteins. PMID 26531155 DOI: 10.1002/Prot.24958  0.334
2015 Boiteux C, Vorobyov I, French RJ, French C, Yarov-Yarovoy V, Allen TW. Sodium Selective Conduction, Inactivation and Inhibition Mechanisms using the Bacterial NavAb Channel Biophysical Journal. 108: 574a. DOI: 10.1016/J.Bpj.2014.11.3141  0.384
2014 Boiteux C, Vorobyov I, French RJ, French C, Yarov-Yarovoy V, Allen TW. Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel. Proceedings of the National Academy of Sciences of the United States of America. 111: 13057-62. PMID 25136136 DOI: 10.1073/Pnas.1408710111  0.402
2014 Boiteux C, Vorobyov I, Allen TW. Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel. Proceedings of the National Academy of Sciences of the United States of America. 111: 3454-9. PMID 24550503 DOI: 10.1073/Pnas.1320907111  0.398
2014 Vorobyov I, Olson TE, Kim JH, Koeppe RE, Andersen OS, Allen TW. Ion-induced defect permeation of lipid membranes. Biophysical Journal. 106: 586-97. PMID 24507599 DOI: 10.1016/J.Bpj.2013.12.027  0.391
2014 Boiteux C, Vorobyov I, Allen TW. The Origins of Ion Selectivity in a Bacterial Sodium Channel Revealed by μS-Long Simulations Biophysical Journal. 106: 131a. DOI: 10.1016/J.Bpj.2013.11.773  0.383
2014 Boiteux C, Vorobyov I, Allen TW. Uncovering the Links Between Conformational Flexibility and Function for a Bacterial Voltage-Gated Sodium Channel Biophysical Journal. 106: 130a. DOI: 10.1016/J.Bpj.2013.11.767  0.4
2014 Chen P, Vorobyov I, Allen TW. Charged Protein-Lipid Interactions in Bilayers with Wide-Ranging Thickness Biophysical Journal. 106: 98a. DOI: 10.1016/J.Bpj.2013.11.613  0.405
2014 Lu J, Vorobyov I, Allen TW. The Distributions and Orientations of Retinoids in Retinal Membranes Studied with All-Atom Molecular Dynamics Simulations Biophysical Journal. 106: 499a. DOI: 10.1016/J.Bpj.2013.11.2793  0.317
2013 Li L, Vorobyov I, Allen TW. The different interactions of lysine and arginine side chains with lipid membranes. The Journal of Physical Chemistry. B. 117: 11906-20. PMID 24007457 DOI: 10.1021/Jp405418Y  0.405
2013 Boiteux C, Vorobyov I, Allen TW. Long Molecular Dynamics Simulations of the Voltage-Gated Sodium Channel, NavAb Biophysical Journal. 104: 137a. DOI: 10.1016/J.Bpj.2012.11.779  0.388
2012 Vorobyov I, Bennett WF, Tieleman DP, Allen TW, Noskov S. The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers. Journal of Chemical Theory and Computation. 8: 618-28. PMID 26596610 DOI: 10.1021/Ct200417P  0.382
2012 Li LB, Vorobyov I, Allen TW. The role of membrane thickness in charged protein-lipid interactions. Biochimica Et Biophysica Acta. 1818: 135-45. PMID 22063722 DOI: 10.1016/J.Bbamem.2011.10.026  0.396
2012 Vorobyov I, Roark MB, Feller SE, Allen TW. Effect of Lipid Unsaturation on Membrane Protein Structure and Function from Multi-Microsecond Molecular Dynamics Simulations Biophysical Journal. 102: 498a. DOI: 10.1016/J.Bpj.2011.11.2725  0.411
2012 Vorobyov I, Koeppe R, Andersen OS, Allen TW. Origins of Non-Selective Ion Transport across Lipid Bilayers Biophysical Journal. 102: 335a. DOI: 10.1016/J.Bpj.2011.11.1834  0.387
2011 Vorobyov I, Allen TW. On the role of anionic lipids in charged protein interactions with membranes. Biochimica Et Biophysica Acta. 1808: 1673-83. PMID 21073855 DOI: 10.1016/J.Bbamem.2010.11.009  0.362
2010 Vorobyov I, Bekker B, Allen TW. Electrostatics of deformable lipid membranes. Biophysical Journal. 98: 2904-13. PMID 20550903 DOI: 10.1016/J.Bpj.2010.03.046  0.384
2010 Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. The Journal of Physical Chemistry. B. 114: 7830-43. PMID 20496934 DOI: 10.1021/Jp101759Q  0.361
2010 Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, Mackerell AD, Roux B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. Journal of Chemical Theory and Computation. 6: 774-786. PMID 20300554 DOI: 10.1021/Ct900576A  0.32
2010 Vorobyov I, Allen TW. The electrostatics of solvent and membrane interfaces and the role of electronic polarizability Journal of Chemical Physics. 132. DOI: 10.1063/1.3402125  0.401
2010 Vorobyov I, Allen TW. On the Roles of Anionic Lipids in Protein Localization and Permeability of Membranes Biophysical Journal. 98: 81a-82a. DOI: 10.1016/J.Bpj.2009.12.461  0.395
2009 Vorobyov I, Bekker B, Allen TW. Electrostatic Determinants of Membrane Ion Permeability Biophysical Journal. 96: 660a. DOI: 10.1016/J.Bpj.2008.12.3490  0.421
2008 Li L, Vorobyov I, Allen TW. Potential of mean force and pKa profile calculation for a lipid membrane-exposed arginine side chain. The Journal of Physical Chemistry. B. 112: 9574-87. PMID 18636765 DOI: 10.1021/Jp7114912  0.427
2008 Vorobyov I, Li L, Allen TW. Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane. The Journal of Physical Chemistry. B. 112: 9588-602. PMID 18636764 DOI: 10.1021/Jp711492H  0.429
2008 Li L, Vorobyov I, MacKerell AD, Allen TW. Is arginine charged in a membrane? Biophysical Journal. 94: L11-3. PMID 17981901 DOI: 10.1529/Biophysj.107.121566  0.426
2008 Li L, Vorobyov I, Dorairaj S, Allen TW. Chapter 15 Charged Protein Side Chain Movement in Lipid Bilayers Explored with Free Energy Simulation Current Topics in Membranes. 60: 405-459. DOI: 10.1016/S1063-5823(08)00015-X  0.408
2007 Anisimov VM, Vorobyov IV, Roux B, Mackerell AD. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. Journal of Chemical Theory and Computation. 3: 1927-1946. PMID 18802495 DOI: 10.1021/Ct700100A  0.317
2006 Harder E, Anisimov VM, Vorobyov IV, Lopes PE, Noskov SY, MacKerell AD, Roux B. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 2: 1587-97. PMID 26627029 DOI: 10.1021/Ct600180X  0.379
2006 Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD. A polarizable model of water for molecular dynamics simulations of biomolecules Chemical Physics Letters. 418: 245-249. DOI: 10.1016/J.Cplett.2005.10.135  0.308
2005 Anisimov VM, Lamoureux G, Vorobyov IV, Huang N, Roux B, MacKerell AD. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 1: 153-68. PMID 26641126 DOI: 10.1021/Ct049930P  0.347
2002 Vorobyov I, Yappert MC, DuPré DB. Energetic and Topological Analyses of Cooperative σH- and πH-Bonding Interactions The Journal of Physical Chemistry A. 106: 10691-10699. DOI: 10.1021/Jp0264580  0.63
2002 Vorobyov I, Yappert MC, DuPré DB. Hydrogen Bonding in Monomers and Dimers of 2-Aminoethanol The Journal of Physical Chemistry A. 106: 668-679. DOI: 10.1021/Jp013211E  0.619
2001 DuPré DB, Vorobyov I, Yappert M. Orbital interactions in stable and metastable conformations of the dimethylphosphate anion Journal of Molecular Structure: Theochem. 544: 91-109. DOI: 10.1016/S0166-1280(01)00389-X  0.638
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