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 |
0.321 |
|
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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