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Serdar Kuyucak - Publications

Affiliations: 
CMCI University of Sydney, Australia 
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45 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
2022 Meng G, Kuyucak S. Computational Design of High-Affinity Blockers for Sodium Channel Na1.2 from μ-Conotoxin KIIIA. Marine Drugs. 20. PMID 35200683 DOI: 10.3390/md20020154  0.467
2021 Wong SL, Awatade NT, Astore MA, Allan KM, Carnell MJ, Slapetova I, Chen PC, Capraro A, Fawcett LK, Whan RM, Griffith R, Ooi CY, Kuyucak S, Jaffe A, Waters SA. Molecular dynamics and functional characterization of I37R-CFTR lasso mutation provide insights into channel gating activity. Iscience. 25: 103710. PMID 35072004 DOI: 10.1016/j.isci.2021.103710  0.378
2020 Ong ST, Bajaj S, Tanner MR, Chang SC, Krishnarjuna B, Ng XR, Morales RAV, Chen MW, Luo D, Patel D, Yasmin S, Ng JJH, Zhuang Z, Nguyen HM, El Sahili A, ... ... Kuyucak S, et al. Modulation of Lymphocyte Potassium Channel K1.3 by Membrane-Penetrating, Joint-Targeting Immunomodulatory Plant Defensin. Acs Pharmacology & Translational Science. 3: 720-736. PMID 32832873 DOI: 10.1021/acsptsci.0c00035  0.557
2020 Patel D, Kuyucak S, Doupnik CA. Structural Determinants Mediating Tertiapin Block of Neuronal Kir3.2 channels. Biochemistry. PMID 31990535 DOI: 10.1021/Acs.Biochem.9B01098  0.614
2018 Rashid MH, Kuyucak S. Computational Study of the Loss-of-Function Mutations in the Kv1.5 Channel Associated with Atrial Fibrillation. Acs Omega. 3: 8882-8890. PMID 31459020 DOI: 10.1021/acsomega.8b01094  0.43
2017 Hung A, Kuyucak S, Schroeder CI, Kaas Q. Modelling the interactions between animal venom peptides and membrane proteins. Neuropharmacology. PMID 28778835 DOI: 10.1016/J.Neuropharm.2017.07.036  0.386
2017 Patel D, Kuyucak S. Computational study of aggregation mechanism in human lysozyme[D67H]. Plos One. 12: e0176886. PMID 28467454 DOI: 10.1371/journal.pone.0176886  0.512
2016 Patel D, Mahdavi S, Kuyucak S. Computational Study of Binding of μ-Conotoxin GIIIA to Bacterial Sodium Channels NaVAb and NaVRh. Biochemistry. 55: 1929-38. PMID 26959170 DOI: 10.1021/acs.biochem.5b01324  0.606
2015 Mahdavi S, Kuyucak S. Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels. Plos One. 10: e0133000. PMID 26274802 DOI: 10.1371/journal.pone.0133000  0.467
2014 Mahdavi S, Kuyucak S. Systematic study of binding of μ-conotoxins to the sodium channel NaV1.4. Toxins. 6: 3454-70. PMID 25529306 DOI: 10.3390/toxins6123454  0.507
2014 Kuyucak S, Norton RS. Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics. Future Medicinal Chemistry. 6: 1645-58. PMID 25406005 DOI: 10.4155/fmc.14.98  0.414
2014 Mahdavi S, Kuyucak S. Molecular dynamics study of binding of µ-conotoxin GIIIA to the voltage-gated sodium channel Na(v)1.4. Plos One. 9: e105300. PMID 25133704 DOI: 10.1371/journal.pone.0105300  0.54
2014 Rashid MH, Huq R, Tanner MR, Chhabra S, Khoo KK, Estrada R, Dhawan V, Chauhan S, Pennington MW, Beeton C, Kuyucak S, Norton RS. A potent and Kv1.3-selective analogue of the scorpion toxin HsTX1 as a potential therapeutic for autoimmune diseases. Scientific Reports. 4: 4509. PMID 24676092 DOI: 10.1038/Srep04509  0.403
2014 Rashid MH, Kuyucak S. Free energy simulations of binding of HsTx1 toxin to Kv1 potassium channels: the basis of Kv1.3/Kv1.1 selectivity. The Journal of Physical Chemistry. B. 118: 707-16. PMID 24397610 DOI: 10.1021/jp410950h  0.47
2013 Rashid MH, Heinzelmann G, Huq R, Tajhya RB, Chang SC, Chhabra S, Pennington MW, Beeton C, Norton RS, Kuyucak S. A potent and selective peptide blocker of the Kv1.3 channel: prediction from free-energy simulations and experimental confirmation. Plos One. 8: e78712. PMID 24244345 DOI: 10.1371/Journal.Pone.0078712  0.42
2013 Rashid MH, Mahdavi S, Kuyucak S. Computational studies of marine toxins targeting ion channels. Marine Drugs. 11: 848-69. PMID 23528952 DOI: 10.3390/md11030848  0.524
2013 Mahdavi S, Kuyucak S. Why the Drosophila Shaker K+ channel is not a good model for ligand binding to voltage-gated Kv1 channels. Biochemistry. 52: 1631-40. PMID 23398369 DOI: 10.1021/bi301257p  0.552
2012 Baştuğ T, Kuyucak S. Molecular dynamics simulations of membrane proteins. Biophysical Reviews. 4: 271-282. PMID 28510077 DOI: 10.1007/s12551-012-0084-9  0.327
2012 Timko J, Kuyucak S. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations. The Journal of Chemical Physics. 137: 205106. PMID 23206041 DOI: 10.1063/1.4768247  0.388
2012 Pennington MW, Harunur Rashid M, Tajhya RB, Beeton C, Kuyucak S, Norton RS. A C-terminally amidated analogue of ShK is a potent and selective blocker of the voltage-gated potassium channel Kv1.3. Febs Letters. 586: 3996-4001. PMID 23063513 DOI: 10.1016/J.Febslet.2012.09.038  0.475
2012 Rashid MH, Kuyucak S. Affinity and selectivity of ShK toxin for the Kv1 potassium channels from free energy simulations. The Journal of Physical Chemistry. B. 116: 4812-22. PMID 22480371 DOI: 10.1021/jp300639x  0.518
2012 Chen PC, Kuyucak S. Developing a comparative docking protocol for the prediction of peptide selectivity profiles: investigation of potassium channel toxins. Toxins. 4: 110-38. PMID 22474570 DOI: 10.3390/toxins4020110  0.392
2011 Baştuğ T, Kuyucak S. Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels. Biophysical Journal. 100: 629-636. PMID 21281577 DOI: 10.1016/j.bpj.2010.12.3718  0.384
2009 Baştuğ T, Kuyucak S. Importance of the peptide backbone description in modeling the selectivity filter in potassium channels. Biophysical Journal. 96: 4006-12. PMID 19450472 DOI: 10.1016/j.bpj.2009.02.041  0.481
2009 Chen PC, Kuyucak S. Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations. Biophysical Journal. 96: 2577-88. PMID 19348743 DOI: 10.1016/j.bpj.2008.12.3952  0.503
2009 Ju P, Pages G, Riek RP, Chen PC, Torres AM, Bansal PS, Kuyucak S, Kuchel PW, Vandenberg JI. The pore domain outer helix contributes to both activation and inactivation of the HERG K+ channel. The Journal of Biological Chemistry. 284: 1000-8. PMID 18996846 DOI: 10.1074/jbc.M806400200  0.386
2008 Baştuğ T, Chen PC, Patra SM, Kuyucak S. Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling. The Journal of Chemical Physics. 128: 155104. PMID 18433285 DOI: 10.1063/1.2904461  0.31
2007 Wijesinghe R, Coorey N, Kuyucak S. Charge state of the fast gate in chloride channels: insights from electrostatic calculations in a schematic model. The Journal of Chemical Physics. 127: 195102. PMID 18035906 DOI: 10.1063/1.2804419  0.39
2007 Patra SM, Baştug T, Kuyucak S. Binding of organic cations to gramicidin A channel studied with AutoDock and molecular dynamics simulations. The Journal of Physical Chemistry. B. 111: 11303-11. PMID 17784747 DOI: 10.1021/jp074228l  0.368
2007 Baştuğ T, Kuyucak S. Free energy simulations of single and double ion occupancy in gramicidin A. The Journal of Chemical Physics. 126: 105103. PMID 17362089 DOI: 10.1063/1.2710267  0.319
2007 Kutteh R, Vandenberg JI, Kuyucak S. Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel. The Journal of Physical Chemistry. B. 111: 1090-8. PMID 17266262 DOI: 10.1021/jp066294d  0.493
2006 Baştuğ T, Patra SM, Kuyucak S. Molecular dynamics simulations of gramicidin A in a lipid bilayer: from structure-function relations to force fields. Chemistry and Physics of Lipids. 141: 197-204. PMID 16600199 DOI: 10.1016/j.chemphyslip.2006.02.012  0.304
2006 Baştuğ T, Gray-Weale A, Patra SM, Kuyucak S. Role of protein flexibility in ion permeation: a case study in gramicidin A. Biophysical Journal. 90: 2285-96. PMID 16415054 DOI: 10.1529/biophysj.105.073205  0.45
2003 Kuyucak S, Bastug T. Physics of ion channels. Journal of Biological Physics. 29: 429-46. PMID 23345858 DOI: 10.1023/A:1027309113522  0.37
2003 Corry B, Kuyucak S, Chung SH. Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels. Biophysical Journal. 84: 3594-606. PMID 12770869 DOI: 10.1016/S0006-3495(03)75091-7  0.329
2003 Baştuğ T, Kuyucak S. Role of the dielectric constants of membrane proteins and channel water in ion permeation. Biophysical Journal. 84: 2871-82. PMID 12719220 DOI: 10.1016/S0006-3495(03)70015-0  0.303
2003 Takahashi T, Kuyucak S. Functional properties of threefold and fourfold channels in ferritin deduced from electrostatic calculations. Biophysical Journal. 84: 2256-63. PMID 12668434 DOI: 10.1016/S0006-3495(03)75031-0  0.391
2003 Allen TW, Baştuğ T, Kuyucak S, Chung SH. Gramicidin A channel as a test ground for molecular dynamics force fields. Biophysical Journal. 84: 2159-68. PMID 12668425 DOI: 10.1016/S0006-3495(03)75022-X  0.379
2002 Kuyucak S, Chung SH. Permeation models and structure-function relationships in ion channels. Journal of Biological Physics. 28: 289-308. PMID 23345776 DOI: 10.1023/A:1019939900568  0.423
2002 Chung SH, Kuyucak S. Recent advances in ion channel research. Biochimica Et Biophysica Acta. 1565: 267-86. PMID 12409200 DOI: 10.1016/s0005-2736(02)00574-6  0.44
2002 Edwards S, Corry B, Kuyucak S, Chung SH. Continuum electrostatics fails to describe ion permeation in the gramicidin channel. Biophysical Journal. 83: 1348-60. PMID 12202360 DOI: 10.1016/S0006-3495(02)73905-2  0.478
2002 Chung SH, Kuyucak S. Ion channels: Recent progress and prospects European Biophysics Journal. 31: 283-293. PMID 12122475 DOI: 10.1007/s00249-002-0216-4  0.423
2002 Chung SH, Allen TW, Kuyucak S. Modeling diverse range of potassium channels with Brownian dynamics. Biophysical Journal. 83: 263-77. PMID 12080118 DOI: 10.1016/S0006-3495(02)75167-9  0.478
2002 Corry B, Hoyles M, Allen TW, Walker M, Kuyucak S, Chung SH. Reservoir boundaries in Brownian dynamics simulations of ion channels. Biophysical Journal. 82: 1975-84. PMID 11916855 DOI: 10.1016/S0006-3495(02)75546-X  0.319
2002 Chung SH, Allen TW, Kuyucak S. Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations. Biophysical Journal. 82: 628-45. PMID 11806907 DOI: 10.1016/S0006-3495(02)75427-1  0.437
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