Toby W. Allen - Publications

Affiliations: 
RMIT University, Melbourne, Victoria, Australia 

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 Ngo V, Li H, MacKerell AD, Allen TW, Roux B, Noskov S. Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel. Journal of Chemical Theory and Computation. PMID 33539082 DOI: 10.1021/acs.jctc.0c00968  0.72
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  0.72
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  0.72
2016 Boiteux C, Allen TW. Understanding Sodium Channel Function and Modulation Using Atomistic Simulations of Bacterial Channel Structures. Current Topics in Membranes. 78: 145-82. PMID 27586284 DOI: 10.1016/bs.ctm.2016.07.002  0.96
2016 Ngo VA, Kim I, Allen TW, Noskov SY. Estimation of Potentials of Mean Force from Non-Equilibrium Pulling Simulations Using Both Minh-Adib Estimator and Weighted Histogram Analysis Method. Journal of Chemical Theory and Computation. PMID 26799775 DOI: 10.1021/acs.jctc.5b01050  0.96
2015 Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, et al. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. The Journal of Membrane Biology. 248: 611-40. PMID 26063070 DOI: 10.1007/s00232-015-9802-0  0.96
2014 Yarov-Yarovoy V, Allen TW, Clancy CE. Computational Models for Predictive Cardiac Ion Channel Pharmacology. Drug Discovery Today. Disease Models. 14: 3-10. PMID 26635886 DOI: 10.1016/j.ddmod.2014.04.001  0.96
2014 Mares LJ, Garcia A, Rasmussen HH, Cornelius F, Mahmmoud YA, Berlin JR, Lev B, Allen TW, Clarke RJ. Identification of electric-field-dependent steps in the Na(+),K(+)-pump cycle. Biophysical Journal. 107: 1352-63. PMID 25229143 DOI: 10.1016/j.bpj.2014.05.054  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2013 de Jesus AJ, Allen TW. The determinants of hydrophobic mismatch response for transmembrane helices. Biochimica Et Biophysica Acta. 1828: 851-63. PMID 22995244 DOI: 10.1016/j.bbamem.2012.09.012  0.96
2013 de Jesus AJ, Allen TW. The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch. Biochimica Et Biophysica Acta. 1828: 864-76. PMID 22989724 DOI: 10.1016/j.bbamem.2012.09.009  0.96
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  0.72
2012 Kim I, Allen TW. Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space. The Journal of Chemical Physics. 136: 164103. PMID 22559466 DOI: 10.1063/1.3701766  0.96
2012 Allen TW, Separovic F. Membrane protein structure and function. Biochimica Et Biophysica Acta. 1818: 125. PMID 22225970 DOI: 10.1016/j.bbamem.2011.12.015  0.96
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  0.96
2012 Vorobyov I, Bennett WFD, 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: 618-628. DOI: 10.1021/ct200417p  0.96
2011 Kim I, Allen TW. On the selective ion binding hypothesis for potassium channels. Proceedings of the National Academy of Sciences of the United States of America. 108: 17963-8. PMID 22011574 DOI: 10.1073/pnas.1110735108  0.96
2011 Nimigean CM, Allen TW. Origins of ion selectivity in potassium channels from the perspective of channel block. The Journal of General Physiology. 137: 405-13. PMID 21518829 DOI: 10.1085/jgp.201010551  0.96
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  0.96
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  0.96
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  0.96
2009 Thompson AN, Kim I, Panosian TD, Iverson TM, Allen TW, Nimigean CM. Mechanism of potassium-channel selectivity revealed by Na(+) and Li(+) binding sites within the KcsA pore. Nature Structural & Molecular Biology. 16: 1317-24. PMID 19946269 DOI: 10.1038/nsmb.1703  0.96
2008 Shreve AP, Howland MC, Sapuri-Butti AR, Allen TW, Parikh AN. Evidence for leaflet-dependent redistribution of charged molecules in fluid supported phospholipid bilayers. Langmuir : the Acs Journal of Surfaces and Colloids. 24: 13250-3. PMID 19007257 DOI: 10.1021/la802909c  0.96
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  0.96
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  0.96
2008 Roux B, Andersen OS, Allen TW. Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)]. The Journal of Chemical Physics. 128: 227101; author reply. PMID 18554067 DOI: 10.1063/1.2931568  0.96
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  0.96
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  0.96
2007 Allen TW. Modeling charged protein side chains in lipid membranes. The Journal of General Physiology. 130: 237-40. PMID 17635964 DOI: 10.1085/jgp.200709850  0.96
2007 Dorairaj S, Allen TW. On the thermodynamic stability of a charged arginine side chain in a transmembrane helix. Proceedings of the National Academy of Sciences of the United States of America. 104: 4943-8. PMID 17360368 DOI: 10.1073/pnas.0610470104  0.96
2006 Allen TW, Andersen OS, Roux B. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Biophysical Chemistry. 124: 251-67. PMID 16781050 DOI: 10.1016/j.bpc.2006.04.015  0.96
2006 Allen TW, Andersen OS, Roux B. Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields. Biophysical Journal. 90: 3447-68. PMID 16500984 DOI: 10.1529/biophysj.105.077073  0.96
2004 Allen TW, Andersen OS, Roux B. On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. The Journal of General Physiology. 124: 679-90. PMID 15572347 DOI: 10.1085/jgp.200409111  0.96
2004 Allen TW, Andersen OS, Roux B. Energetics of ion conduction through the gramicidin channel. Proceedings of the National Academy of Sciences of the United States of America. 101: 117-22. PMID 14691245 DOI: 10.1073/pnas.2635314100  0.96
2003 Allen TW, Andersen OS, Roux B. Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. Journal of the American Chemical Society. 125: 9868-77. PMID 12904055 DOI: 10.1021/ja029317k  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2001 Allen TW, Chung SH. Brownian dynamics study of an open-state KcsA potassium channel. Biochimica Et Biophysica Acta. 1515: 83-91. PMID 11718664 DOI: 10.1016/S0005-2736(01)00395-9  0.96
2001 Corry B, Allen TW, Kuyucak S, Chung SH. Mechanisms of permeation and selectivity in calcium channels. Biophysical Journal. 80: 195-214. PMID 11159395 DOI: 10.1016/S0006-3495(01)76007-9  0.96
2001 Bliznyuk AA, Rendell AP, Allen TW, Chung SH. The potassium ion channel: Comparison of linear scaling semiempirical and molecular mechanics representations of the electrostatic potential Journal of Physical Chemistry B. 105: 12674-12679. DOI: 10.1021/jp013069h  0.96
2000 Corry B, Allen TW, Kuyucak S, Chung SH. A model of calcium channels. Biochimica Et Biophysica Acta. 1509: 1-6. PMID 11118513 DOI: 10.1016/S0005-2736(00)00330-8  0.96
2000 Allen TW, Kuyucak S, Chung SH. Molecular dynamics estimates of ion diffusion in model hydrophobic and KcsA potassium channels. Biophysical Chemistry. 86: 1-14. PMID 11011695 DOI: 10.1016/S0301-4622(00)00153-8  0.96
1999 Chung SH, Allen TW, Hoyles M, Kuyucak S. Permeation of ions across the potassium channel: Brownian dynamics studies. Biophysical Journal. 77: 2517-33. PMID 10545353 DOI: 10.1016/S0006-3495(99)77087-6  0.96
1999 Allen TW, Kuyucak S, Chung SH. Molecular dynamics study of the KcsA potassium channel. Biophysical Journal. 77: 2502-16. PMID 10545352 DOI: 10.1016/S0006-3495(99)77086-4  0.96
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