I. Vorobyov

发表

Molecular Dynamics Computations for Proteins: A Case Study in Membrane Ion Permeation

I. Vorobyov, T. Allen, 2009 .

Refining the treatment of membrane proteins by coarse‐grained models

Arieh Warshel, Igor Vorobyov, Ilsoo Kim, 2016, Proteins.

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

Alexander D. MacKerell, Jeffery B. Klauda, D. Tobias, 2010, The journal of physical chemistry. B.

A polarizable model of water for molecular dynamics simulations of biomolecules

Alexander D. MacKerell, Edward D Harder, B. Roux, 2006 .

Selectivity filter modalities and rapid inactivation of the hERG1 channel

Williams E. Miranda, H. Duff, I. Vorobyov, 2020, Proceedings of the National Academy of Sciences.

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

Kevin R. DeMarco, Slava Bekker, Igor Vorobyov, 2018, The Journal of physiology.

Energetic and Topological Analyses of Cooperative σH- and πH-Bonding Interactions

I. Vorobyov, M. Yappert, D. B. Dupre, 2002 .

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

Kevin R. DeMarco, Junko Kurokawa, Pei-Chi Yang, 2017, The Journal of physiology.

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

Toby W Allen, Igor Vorobyov, I. Vorobyov, 2014, Proceedings of the National Academy of Sciences.

A Computational Pipeline to Predict Cardiotoxicity

Kevin R. DeMarco, V. Yarov-Yarovoy, I. Vorobyov, 2020, Circulation research.

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

Kevin R. DeMarco, V. Yarov-Yarovoy, I. Vorobyov, 2018, Proceedings of the National Academy of Sciences.

Orbital interactions in stable and metastable conformations of the dimethylphosphate anion

I. Vorobyov, M. Yappert, D. B. Dupre, 2001 .

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

Toby W Allen, Igor Vorobyov, I. Vorobyov, 2008, The journal of physical chemistry. B.

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

I. Vorobyov, D. Borchman, M. Yappert, 2000, Biochimica et biophysica acta.

Conformational studies of sphingolipids by NMR spectroscopy. I. Dihydrosphingomyelin.

I. Vorobyov, D. Borchman, M. Yappert, 2000, Biochimica et biophysica acta.

A deep learning algorithm to translate and classify cardiac electrophysiology: From induced pluripotent stem cell-derived cardiomyocytes to adult cardiac cells

Colleen E. Clancy, Yasunari Kanda, Junko Kurokawa, 2020 .

A deep learning algorithm to translate and classify cardiac electrophysiology: From iPSC-CMs to adult cardiac cells

Divya C. Kernik, I. Vorobyov, C. Clancy, 2020 .

Sex, drugs, and funky rhythms.

I. Vorobyov, C. Clancy, 2018, Heart rhythm.

Exploring the free-energy landscape of GPCR activation

Arieh Warshel, Raphael Alhadeff, Igor Vorobyov, 2018, Proceedings of the National Academy of Sciences.

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

Alexander D. MacKerell, Sibsankar Kundu, Chayan Acharya, 2009, J. Comput. Chem..

Hydrogen Bonding in Monomers and Dimers of 2-Aminoethanol

Igor Vorobyov, Donald B. DuPré, I. Vorobyov, 2002 .

Electrostatics of deformable lipid membranes.

I. Vorobyov, T. Allen, Borislava Bekker, 2010, Biophysical journal.

Chapter 15 Charged Protein Side Chain Movement in Lipid Bilayers Explored with Free Energy Simulation

I. Vorobyov, T. Allen, Libo Li, 2008 .

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

I. Vorobyov, T. Allen, Libo Li, 2013, The journal of physical chemistry. B.

Ion-induced defect permeation of lipid membranes.

Toby W Allen, Igor Vorobyov, Olaf S Andersen, 2014, Biophysical journal.

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

I. Vorobyov, D. Borchman, M. Yappert, 2003, Experimental eye research.

Molecular determinants of pro-arrhythmia proclivity of d- and l-sotalol via a multi-scale modeling pipeline

Kevin R. DeMarco, Jon T. Sack, J. Fettinger, 2021, Journal of molecular and cellular cardiology.

The electrostatics of solvent and membrane interfaces and the role of electronic polarizability

Igor Vorobyov, I. Vorobyov, T. Allen, 2010 .

Elucidating Molecular Mechanisms of Protoxin-2 State-specific Binding to the Human NaV1.7 Channel

V. Yarov-Yarovoy, I. Vorobyov, H. Wulff, 2023, bioRxiv.

Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation.

I. Vorobyov, T. Allen, B. Lev, 2019, Chemical reviews.

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

I. Vorobyov, T. Allen, 2011, Biochimica et biophysica acta.

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

Toby W Allen, Vladimir Yarov-Yarovoy, Igor Vorobyov, 2014, Proceedings of the National Academy of Sciences.

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

I. Vorobyov, T. Allen, Libo Li, 2012, Biochimica et biophysica acta.

A deep learning algorithm to translate and classify cardiac electrophysiology

Divya C. Kernik, I. Vorobyov, C. Clancy, 2021, eLife.

A deep learning algorithm to translate and classify cardiac electrophysiology: From induced pluripotent stem cell-derived cardiomyocytes to adult cardiac cells

Divya C. Kernik, I. Vorobyov, C. Clancy, 2020 .

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

Alexander D. MacKerell, Adam Moser, Alexander D MacKerell, 2007, Journal of chemical theory and computation.

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

Alexander D. MacKerell, Benoît Roux, Guillaume Lamoureux, 2010, Journal of chemical theory and computation.

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

Toby W Allen, Igor Vorobyov, I. Vorobyov, 2008, The journal of physical chemistry. B.

A computational pipeline to predict cardiotoxicity: From the atom to the rhythm

Kevin R. DeMarco, Colleen E. Clancy, Vladimir Yarov-Yarovoy, 2019, bioRxiv.

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

Alexander D. MacKerell, Benoît Roux, Alexander D Mackerell, 2007, Journal of chemical theory and computation.

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

Alexander D. MacKerell, Benoît Roux, Niu Huang, 2005, Journal of chemical theory and computation.

Atomistic modeling towards predictive cardiotoxicity

Kevin R. DeMarco, John R.D. Dawson, Slava Bekker, 2019, bioRxiv.

Structural modeling of the hERG potassium channel and associated drug interactions

Kevin R. DeMarco, Jon T. Sack, V. Yarov-Yarovoy, 2021, bioRxiv.

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

W F Drew Bennett, Toby W Allen, Igor Vorobyov, 2012, Journal of chemical theory and computation.

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

Kevin R. DeMarco, Slava Bekker, Colleen E. Clancy, 2018, Front. Pharmacol..

A multiscale predictive digital twin for neurocardiac modulation

Kevin R. DeMarco, C. Ripplinger, I. Vorobyov, 2023, The Journal of physiology.

Elucidating Molecular Mechanisms of Protoxin-2 State-specific Binding to the Human NaV1.7 Channel

V. Yarov-Yarovoy, I. Vorobyov, H. Wulff, 2023, bioRxiv.

Charging the Quantum Capacitance of Graphene with a Single Biological Ion Channel

I. Vorobyov, T. Allen, S. Bezrukov, 2014 .

Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist, and stimulatory G protein

V. Yarov-Yarovoy, I. Vorobyov, C. Clancy, 2023, Proceedings of the National Academy of Sciences of the United States of America.

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

Alexander D. MacKerell, Alexander D MacKerell, Victor M Anisimov, 2005, The journal of physical chemistry. B.

Modeling Stereospecific Drug Interactions with Beta-Adrenergic Receptors

Kevin R. DeMarco, V. Yarov-Yarovoy, I. Vorobyov, 2023, bioRxiv.

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

I. Vorobyov, T. Allen, Libo Li, 2013, The journal of physical chemistry. B.

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

Kevin R. DeMarco, Ilkay Altintas, Rommie E. Amaro, 2019, PLoS Comput. Biol..

Structural modeling of hERG channel–drug interactions using Rosetta

Kevin R. DeMarco, Jon T. Sack, V. Yarov-Yarovoy, 2023, Frontiers in pharmacology.

Rearrangement of a unique Kv1.3 selectivity filter conformation upon binding of a drug

K. Chandy, I. Vorobyov, S. Bhushan, 2022, Proceedings of the National Academy of Sciences.

Atomistic mechanisms of the regulation of small-conductance Ca2+-activated K+ channel (SK2) by PIP2.

V. Yarov-Yarovoy, I. Vorobyov, E. Yamoah, 2024, Proceedings of the National Academy of Sciences of the United States of America.