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Institute for Quantum Science and Technology

Publications by S. Y. Noskov

Refereed Journal Publications

20214 publications
  1. W. E. Miranda, J.-Q. Guo, H. Mesa-Galloso, V. Corradi, J. Lees-Miller, D. P. Tieleman, H. J. Duff and S. Y. Noskov, Lipid regulation of hERG1 channel function, Nature Communications 12: 1409 (10 pp.), 3 March 2021.
  2. D. Kerk, M. E. Valdés-Tresanco, R. A. Toth, S. Y. Noskov, K. K.-S. Ng and G. B. Moorhead, Origin of the Phosphoprotein Phosphatase (PPP) sequence family in Bacteria: Critical ancestral sequence changes, radiation patterns and substrate binding features, BBA Advances 1(10): 10005, 18 February 2021.
  3. V. A. Ngo, H. Li, A. D. Mackerell, T. W. Allen, B. Roux and S. Y. Noskov, Polarization effects in water-mediated selective cation transport across a narrow transmembrane channel, Journal of Chemical Theory and Computation 17(3): 1726 - 1741, 4 February 2021.
  4. H. M. Khan, J.-Q. Guo, H. J. Duff, D. P. Tieleman and S. Y. Noskov, Refinement of a cryo-EM structure of hERG: Bridging structure and function, Biophysical Journal 120(4): 738 - 748, 19 January 2021.
202011 publications
  1. M. Queralt-Martín, D. P. Hoogerheide, S. Y. Noskov, A. M. Berezhkovskii, T. K. Rostovtseva and S. M. Bezrukov, VDAC gating thermodynamics, but not gating kinetics, are virtually temperature independent, Biophysical Journal 119(12): 2584 - 2592, 15 December 2020.
  2. M. Mousaei, M. Kudaibergenova, A. D. Mackerell and S. Y. Noskov, Assessing hERG1 blockade from Bayesian machine-learning-optimized site identification by ligand competitive saturation simulations, Journal of Chemical Information and Modeling 60(12): 6489 - 6501, 16 November 2020.
  3. K. S. Amin, X.-J. Hu, D. R. Salahub, C. Baldauf, C. Lim and S. Y. Noskov, Benchmarking polarizable and non-polarizable force fields for Ca2+–peptides against a comprehensive QM dataset , Journal of Chemical Physics 153(14): 144102 (16 pp.), 8 October 2020.
  4. Y.-Y. Zhang, K. Haider, D. Kaur, V. A. Ngo, X.-H. Cai, J.-J. Mao, U. Khaniya, X.-Y. Zhu, S. Y. Noskov, T. Lazaridis and M. R. Gunner, Characterizing the water wire in the Gramicidin channel found by Monte Carlo sampling using continuum electrostatics and in molecular dynamics trajectories with conventional or polarizable force fields, Journal of Computational Biophysics and Chemistry 20(2): 111 - 130, 4 July 2020.
  5. M. Kudaibergenova, J.-Q. Guo, H. M. Khan, F. Zahid, J. Lees-Miller, S. Y. Noskov and H. J. Duff, Allosteric coupling between drug binding and the aromatic cassette in the pore domain of the hERG1 channel: Implications for a state-dependent blockade, Frontiers in Pharmacology 11: 914 (14 pp.), 30 June 2020.
  6. H. R. Zhekova, T. Sakuma, R. Johnson, S. C. Concilio, P. J. Lech, I. Zdravkovic, M. Damergi, L. Suksanpaisan, K.-W. Peng, S. J. Russell and S. Y. Noskov, Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS), Journal of Chemical Information and Modeling 60(3): 1652 - 1665, 5 March 2020.
  7. P.-C. Yang, K. R. DeMarco, P. Aghasafari, M.-T. Jeng, J. R. D. Dawson, S. Bekker, S. Y. Noskov, V. Yarov-Yarovoy, I. Vorobyov and C. E. Clancy, A computational pipeline to predict cardiotoxicity, Circulation Research 126(8): 947 - 964, 24 February 2020.
  8. S. C. Concilio, H. R. Zhekova, S. Y. Noskov and S. J. Russell, Inter-species variation in monovalent anion substrate selectivity and inhibitor sensitivity in the sodium iodide symporter (NIS), PLOS ONE 15(2): e0229085 (25 pp.), 21 February 2020.
  9. L. Kao, R. Azimov, X. M. Shao, N. Abuladze, D. Newman, H. R. Zhekova, S. Y. Noskov, A. Pushkin and I. Kurtz, SLC4A11 function: evidence for H+(OH−) and NH3-H+ transport, American Journal of Cell Physiology 318: C392 - C405, 6 February 2020.
  10. W. E. Miranda, K. R. DeMarco, J.-Q. Guo, H. J. Duff, I. Vorobyov, C. E. Clancy and S. Y. Noskov, Selectivity filter modalities and rapid inactivation of the hERG1 channel, Proceedings of the National Academy of Sciences of the United States of America 117(6): 2795 - 2804, 24 January 2020.
  11. D. Malhotra, M. Jung, C. Fecher-Trost, M. Lovatt, G. S. L. Peh, S. Y. Noskov, J. S. Mehta, R. Zimmermann and J. R. Casey, Defective cell adhesion function of solute transporter, SLC4A11, in endothelial corneal dystrophies, Human Molecular Genetics 29(1): 97 - 116, 1 January 2020.
20194 publications
  1. T. H. Nguyen, V. A. Ngo, J. Paulo Castro Zerba, S. Y. Noskov and D. D. L. Minh, Nonequilibrium path-ensemble averages for symmetric protocols, Journal of Chemical Physics 151(19): 194103 (12 pp.), 18 November 2019.
  2. Y.-B. Wang, R. K. Finol-Urdaneta, V. A. Ngo, R. J. French and S. Y. Noskov, Bases of bacterial sodium channel selectivity among organic cations, Scientific Reports 9: 15260 (12 pp.), 24 October 2019.
  3. L. L. Perissinotti, J.-Q. Guo, M. Kudaibergenova, J. Lees-Miller, M. Ol'khovich, A. Sharapova, G. Perlovich, D. Muruve, B. Gerull, S. Y. Noskov and H. J. Duff, The pore-lipid interface: Role of amino-acid determinants of lipophilic access by ivabradine to the hERG1 pore domain, Molecular Pharmacology 96(2): 259 - 271, 13 August 2019.
  4. V. Corradi, B. I. Sejdiu, H. Mesa-Galloso, S. Y. Noskov, S. J. Marrink and D. P. Tieleman, Emerging diversity in lipid–protein interactions, Chemical Reviews 119(9): 5775 - 5848, 13 February 2019.
20186 publications
  1. V. A. Ngo, J. K. Fanning and S. Y. Noskov, Comparative analysis of protein hydration from MD simulations with additive and polarizable force fields, Advanced Theory and Simulations 2(2): 1800106 (13 pp.), 8 November 2018.
  2. D. P. Hoogerheide, S. Y. Noskov, A. J. Kuszak, S. K. Buchanan, T. K. Rostovtseva and H. Nanda, Structure of voltage-dependent anion channel-tethered bilayer lipid membranes determined using neutron reflectivity, Acta Crystallographica Section D: Structural Biology 74(12): 1219 - 1232, 30 October 2018.
  3. W. E. Miranda, V. A. Ngo, R.-W. Wang, L. Zhang, S. R. W. Chen and S. Y. Noskov, Molecular mechanism of conductance enhancement in narrow cation-selective membrane channels, Journal of Physical Chemistry Letters 9(12): 3497 - 3502, 10 June 2018.
  4. M. Kudaibergenova, L. L. Perissinotti and S. Y. Noskov, Lipid roles in hERG function and interactions with drugs, Neuroscience Letters 700: 70 - 77, 27 May 2018.
  5. S. Wacker and S. Y. Noskov, Performance of machine learning algorithms for qualitative and quantitative prediction drug blockade of hERG1 channel, Computational Toxicology 6: 55 - 63, 8 May 2018.
  6. L. L. Perissinotti, P. M. De Biase, J.-Q. Guo, P.-C. Yang, M. C. Lee, C. E. Clancy, H. J. Duff and S. Y. Noskov, Determinants of isoform-specific gating kinetics of hERG1 channel: Combined experimental and simulation study, Frontiers in Physiology 9: 207 (20 pp.), 12 April 2018.
20175 publications
  1. H. R. Zhekova, V. A. Ngo, M. C. da Silva, D. R. Salahub and S. Y. Noskov, Selective ion binding and transport by membrane proteins – A computational perspective, Coordination Chemistry Reviews 345: 108 - 136, 15 August 2017. (Special issue on Chemical Bonding in Inorganic Specials "State of Art" Coordination Chemistry Review, 50 Years of Progress).
  2. V. A. Ngo, L. L. Perissinotti, W. E. Miranda, W. Chen and S. Y. Noskov, Mapping ryanodine binding sites in the pore cavity of ryanodine receptors, Biophysical Journal 112: 1 - 9, 25 April 2017. (accepted or in press).
  3. D. Serdar, E. Ismail, R. E. Salmas, M. Patterson and S. Y. Noskov, First universal pharmacophore model for hERG1 K+ channel activators, Journal of Molecular Graphics and Modelling, 5 April 2017. (accepted or in press).
  4. E. Grandi, M. C. Sanguinetti, D. C. Bartos, D. M. Bers, Y. Chen-Izu, N. Chiamvimonvat, H. M. Colecraft, B. P. Delisle, J. Heijman, M. F. Navedo, S. Y. Noskov, C. Proenza, J. I. Vandenberg and V. Yarov-Yarovoy, Potassium channels in the heart: structure, function and regulation, Journal of Physiology 595(7): 2209 - 2228, 1 April 2017.
  5. A. N. Bukiya, S. Durdagi, S. Y. Noskov and A. Rosenhouse-Dantsker, Cholesterol up-regulates neuronal G protein-gated inwardly rectifying potassium (GIRK) channel activity in the hippocampus, Journal of Biological Chemistry, 17 February 2017. (accepted or in press).
201611 publications
  1. H. R. Zhekova, C.-F Zhao, P. P. M. Schnetkamp and S. Y. Noskov, Characterization of the cation binding sites in the NCKX2 Na+/Ca2+-K+ exchanger, Biochemistry 55(46): 6445 - 6455, 2 November 2016.
  2. Y.-B. Wang, J.-Q. Guo, L. L. Perissinotti, J. Lees-Miller, G. Teng, S. Durdagi, H. J. Duff and S. Y. Noskov, Role of the pH in state-dependent blockade of hERG currents, Scientific Reports 6(3): 32536 (10 pp.), 12 October 2016.
  3. F. Qiu, A. Chamberlin, B. M. Watkins, A. lonescu, M. E. Perez, R. Barro-Soria, C. GonzĂĄlez, S. Y. Noskov and H. P. Larsson, Molecular mechanism of Zn2+ inhibition of a voltage-gated proton channel, Proceedings of the National Academy of Sciences of the United States of America 113(40): 5962 - 5971, 19 September 2016.
  4. S. Y. Noskov, T. K. Rostovtseva, A. Chamberlin, O. Teijido, W. Jiang and S. M. Bezrukov, Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC), Biochimica et Biophysica Acta (BBA)-Biomembranes 1858(7): 1778 - 1790, 31 July 2016.
  5. W. E. Miranda, V. A. Ngo, P. A. Valiente and S. Y. Noskov, Improved QM/MM linear-interaction energy model for substrate recognition in zinc-containing metalloenzymes, Journal of Physical Chemistry B 120(32): 7824 - 7835, 22 July 2016.
  6. P. M. De Biase, E. N. Ervin, P. Pal, O. Samoylova, S. Markosyan, M. G. Keehan, G. A. Barrall and S. Y. Noskov, What controls open-pore and residual currents in the first sensing zone of alpha-hemolysin nanopore? Combined experimental and theoretical study, Nanoscale 8: 11571 - 11579, 9 May 2016.
  7. C. J. F. Solano, K. R. Pothula, J. D. Prajapati, P. M. De Biase, S. Y. Noskov and U. Kleinekathöfer, BROMOCEA code: An improved grand canonical monte carlo/brownian dynamics algorithm including explicit atoms, Journal of Chemical Theory and Computation 12(5): 2401 - 2417, 18 April 2016.
  8. P.-C. Yang, J. D. Moreno, C. Y. Miyake, S. B. Vaughn-Behrens, M.-T. Jeng, G. Randall, X. H. T. Wehrens, S. Y. Noskov and C. E. Clancy, In silico prediction of drug therapy in catecholaminergic polymorphic ventricular tachycardia, Journal of Physiology 594(3): 567 - 593, 1 February 2016.
  9. V. A. Ngo, I. Kim, T. W. Allen and S. Y. Noskov, Estimation of potentials of mean force from nonequilibrium pulling simulations using both minh-adib estimator and weighted histogram analysis method, Journal of Chemical Theory and Computation 12(3): 1000 - 1010, 22 January 2016.
  10. V. A. Ngo, Y.-B. Wang, S. Haas, S. Y. Noskov and R. Farley, K+ block is the mechanism of functional asymmetry in bacterial Nav channels, PLoS Computational Biology 12(1): e1004482 (19 pp.), 4 January 2016.
  11. R. E. Salmas, A. Unlu, M. Yurtsever, S. Y. Noskov and S. Durdagi, In silico investigation of PARP-1 catalytic domains in holo and apo states for the design of high-affinity PARP-1 inhibitors, Journal of Enzyme Inhibition and Medicinal Chemistry 31(1): 112 - 120, 2 January 2016.
20154 publications
  1. N. Manin, I. Zdravkovic, M. C. da Silva, O. Eliseeva, A. Dyshin, O. Yasar, D. R. Salahub, A. M. Kolker, M. G. Kiselev and S. Y. Noskov, LiCl solvation in N-methyl-Acetamide (NMA) as a model for understanding of Li+ binding to amide plane, Physical Chemistry Chemical Physics 18(5): 4191 - 4200, 7 December 2015.
  2. V. A. Ngo, M. X. Silva, M. Kubilius, H. Li, M. Elstner, B. Roux, Q. Cui, D. R. Salahub and S. Y. Noskov, Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins, Journal of Chemical Theory and Computation 11(10): 4992 - 5001, 22 September 2015.
  3. D. R. Salahub, S. Y. Noskov, B. B. Lev, R. Zhang, V. A. Ngo, A. Goursot, P. Calaminici, A. M. Köster, A. Alvarez-Ibarra, D. MejĂ­a-RodrĂ­guez, J. Řezáč, F. Cailliez and A. de la Lande, QM/MM calculations with deMon2k, Molecules 20(3): 4780 - 4812, 16 March 2015.
  4. H. Li, V. A. Ngo, M. C. da Silva, D. R. Salahub, K. Kallahan, B. Roux and S. Y. Noskov, Representation of ion-protein interactions using the Drude polarizable force-field, Journal of Physical Chemistry B special issue: A - P, 10 January 2015.
20101 publication
  1. B. B. Lev, D. R. Salahub and S. Y. Noskov, Na(+), K (+) and Tl(+) hydration from QM/MM computations and MD simulations with a polarizable force field., Interdisciplinary sciences, computational life sciences 2(1): 12 - 20, 28 January 2010.
20091 publication
  1. L. E. V. Bogdan, R. Zhang, A. de la Lande, D. R. Salahub and S. Y. Noskov, The QM-MM interface for CHARMM-deMon, Journal of Computational Chemistry 31(5): 1015 - 1023, 21 December 2009.

Book Chapters

20211 publication
  1. S. B. Dwadasi, K. S. Amin, D. R. Salahub and S. Y. Noskov, QM/MM simulations of proteins: Is explicit inclusion of polarization on the horizon?, Chapter 3, section in book: Multiscale Dynamics Simulations: Nano and Nano-bio Systems in Complex Environments , Dennis R. Salahub & D.-Q. Wei, eds., 2021 (ISBN 978-1-83916-178-0). published by Royal Society of Chemistry.
20161 publication
  1. L. R. Perez, S. Y. Noskov and C. E. Clancy, Computational modeling of cardiac K+ channels and channelopathies, section in book: Ion Channels in Health and Disease, Geoffrey S. Pitt, eds., Chapter 12: 293 - 330, 2016 (ISBN 978-0-12-802002-9). Elsevier.