| Year |
Citation |
Score |
| 2022 |
Saunders M, Wineman-Fisher V, Jakobsson E, Varma S, Pandit SA. High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 35192365 DOI: 10.1021/acs.langmuir.1c03105 |
0.489 |
|
| 2020 |
Wineman-Fisher V, Delgado JM, Nagy PR, Jakobsson E, Pandit SA, Varma S. Transferable interactions of Li and Mg ions in polarizable models. The Journal of Chemical Physics. 153: 104113. PMID 32933310 DOI: 10.1063/5.0022060 |
0.539 |
|
| 2019 |
Kruczek J, Chiu SW, Varma S, Jakobsson E, Pandit S. Interactions of Mono and Di-valent cations at Palmitoyl-Oleoyl-Phosphatidylcholine Interface. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 31337218 DOI: 10.1021/Acs.Langmuir.9B01275 |
0.479 |
|
| 2017 |
Jakobsson E, Argüello-Miranda O, Chiu SW, Fazal Z, Kruczek J, Nunez-Corrales S, Pandit S, Pritchet L. Towards a Unified Understanding of Lithium Action in Basic Biology and its Significance for Applied Biology. The Journal of Membrane Biology. PMID 29127487 DOI: 10.1007/S00232-017-9998-2 |
0.317 |
|
| 2017 |
Palaniappan A, Jakobsson E. Fourier Analysis of Conservation Patterns in Protein Secondary Structure. Computational and Structural Biotechnology Journal. 15: 265-270. PMID 28316759 DOI: 10.1016/J.Csbj.2017.02.002 |
0.37 |
|
| 2017 |
Kruczek J, Chiu SW, Jakobsson E, Pandit SA. Effects of Lithium and Other Monovalent Ions on Palmitoyl Oleoyl Phosphatidylcholine Bilayer. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 28076953 DOI: 10.1021/Acs.Langmuir.6B04166 |
0.341 |
|
| 2017 |
Kruczek J, Chiu S, Jakobsson E, Pandit SA. Unique Modification of Membrane Structure by Lithium: A Molecular Dynamics Study Biophysical Journal. 112: 42a. DOI: 10.1016/J.Bpj.2016.11.267 |
0.336 |
|
| 2016 |
Liu H, Robinson GE, Jakobsson E. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. Plos Computational Biology. 12: e1004921. PMID 27359102 DOI: 10.1371/Journal.Pcbi.1004921 |
0.304 |
|
| 2014 |
Fogarty J, Chiu S, Jakobsson E, Pandit S. Optimization of Coarse-Grained Water-Ion Interaction Parameters for Biological Simulation Biophysical Journal. 106: 406a. DOI: 10.1016/J.Bpj.2013.11.2287 |
0.302 |
|
| 2013 |
Zhou H, Jakobsson E. Predicting protein-protein interaction by the mirrortree method: possibilities and limitations. Plos One. 8: e81100. PMID 24349035 DOI: 10.1371/Journal.Pone.0081100 |
0.413 |
|
| 2013 |
Li Y, Liu H, Rata I, Jakobsson E. Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment. Journal of Chemical Information and Modeling. 53: 500-8. PMID 23336295 DOI: 10.1021/Ci300207X |
0.355 |
|
| 2013 |
Fogarty J, Chiu S, Jakobsson E, Pandit S. Optimization of a Coarse-Grained Force Field for Biological Simulations Biophysical Journal. 104: 506a. DOI: 10.1016/J.Bpj.2012.11.2796 |
0.321 |
|
| 2013 |
Rendon G, Mashl RJ, Saladi S, Jakobsson E. Bacterial Roots and Branches of the HCN/CNG Family of Ion Channels: Phylogeny, Structure, and Implications for Eukaryotic HCN/CNG Structure and Function Biophysical Journal. 104: 278a. DOI: 10.1016/J.Bpj.2012.11.1560 |
0.725 |
|
| 2012 |
Chiu S, Jakobsson E. Coarse Grained Ion-Ion and Ion-Water Interactions Biophysical Journal. 102: 169a. DOI: 10.1016/J.Bpj.2011.11.919 |
0.32 |
|
| 2012 |
Liu H, Li Y, Rata I, Jakobsson E. A Next Step in Protein Secondary Structure Prediction Biophysical Journal. 102: 619a. DOI: 10.1016/J.Bpj.2011.11.3372 |
0.338 |
|
| 2011 |
Rendon G, Kantorovitz MR, Tilson JL, Jakobsson E. Identifying bacterial and archaeal homologs of pentameric ligand-gated ion channel (pLGIC) family using domain-based and alignment-based approaches. Channels (Austin, Tex.). 5: 325-43. PMID 21918370 DOI: 10.4161/Chan.5.4.16822 |
0.381 |
|
| 2011 |
Zhao G, Subbaiah PV, Chiu SW, Jakobsson E, Scott HL. Conjugated double bonds in lipid bilayers: a molecular dynamics simulation study. Chemistry and Physics of Lipids. 164: 251-7. PMID 21320475 DOI: 10.1016/J.Chemphyslip.2011.02.002 |
0.3 |
|
| 2010 |
Ger MF, Rendon G, Tilson JL, Jakobsson E. Domain-based identification and analysis of glutamate receptor ion channels and their relatives in prokaryotes. Plos One. 5: e12827. PMID 20949136 DOI: 10.1371/Journal.Pone.0012827 |
0.617 |
|
| 2010 |
Toghraee R, Lee KI, Papke D, Chiu SW, Jakobsson E, Ravaioli U. SIMULATION OF ION CONDUCTION IN α-HEMOLYSIN NANOPORES WITH COVALENTLY ATTACHED β-CYCLODEXTRIN BASED ON BOLTZMANN TRANSPORT MONTE CARLO MODEL. Journal of Computational and Theoretical Nanoscience. 7: 2555-2567. PMID 20938493 DOI: 10.1166/Jctn.2010.1642 |
0.383 |
|
| 2010 |
Natarajan S, Mashl RJ, Jakobsson E. Evolutionary coupling in the K(V)1.2-β₂ complex. Channels (Austin, Tex.). 4: 355-74. PMID 20818181 DOI: 10.4161/Chan.4.5.12813 |
0.588 |
|
| 2010 |
Lee KI, Toghraee R, Jakobsson E, Ravaioli U. A study of Brownian dynamics simulation for ion transport through a transmembrane pore with a molecular adapter Journal of Computational and Theoretical Nanoscience. 7: 2547-2554. DOI: 10.1166/Jctn.2010.1641 |
0.309 |
|
| 2010 |
Jakobsson E, Rendon G, Kantorovitz R, Tilson J, Ger M. Using Domain Based Discovery Methods to Identify Prokaryotic Counterparts to Eukaryotic Protein Ion Channels Biophysical Journal. 98: 709a. DOI: 10.1016/J.Bpj.2009.12.3891 |
0.614 |
|
| 2010 |
Mashl RJ, Jakobsson E. Phases, Transport, and Dielectric Properties of Water Confined in Nanoscale Channels Biophysical Journal. 98: 540a. DOI: 10.1016/J.Bpj.2009.12.2932 |
0.383 |
|
| 2010 |
Natarajan S, Mashl J, Jakobsson E. Evolutionary coupling in the KV1.2-β2 complex Channels. 4. |
0.404 |
|
| 2009 |
Toghraee R, Mashl RJ, Lee KI, Jakobsson E, Ravaioli U. Simulation of charge transport in ion channels and nanopores with anisotropic permittivity. Journal of Computational Electronics. 8: 98-109. PMID 20445807 DOI: 10.1007/S10825-009-0272-4 |
0.403 |
|
| 2009 |
Natarajan S, Jakobsson E. Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. Plos One. 4: e5898. PMID 19521530 DOI: 10.1371/Journal.Pone.0005898 |
0.523 |
|
| 2009 |
Rendon G, Ger MF, Kantorovitz R, Natarajan S, Tilson J, Jakobsson E. Understanding the "horizontal dimension" of Molecular evolution to annotate, classify, and discover proteins with functional domains Journal of Computer Science and Technology. 25: 82-94. DOI: 10.1007/S11390-010-9307-3 |
0.655 |
|
| 2008 |
Mashl RJ, Jakobsson E. End-point targeted molecular dynamics: large-scale conformational changes in potassium channels. Biophysical Journal. 94: 4307-19. PMID 18310251 DOI: 10.1529/Biophysj.107.118778 |
0.365 |
|
| 2008 |
Pandit SA, Chiu Sw, Jakobsson E, Scott HL. Chapter 10 Atomistic and Mean Field Simulations of Lateral Organization in Membranes Current Topics in Membranes. 60: 281-312. DOI: 10.1016/S1063-5823(08)00010-0 |
0.312 |
|
| 2007 |
Tseng TT, McMahon AM, Johnson VT, Mangubat EZ, Zahm RJ, Pacold ME, Jakobsson E. Sodium channel auxiliary subunits. Journal of Molecular Microbiology and Biotechnology. 12: 249-62. PMID 17587873 DOI: 10.1159/000099646 |
0.613 |
|
| 2007 |
Varma S, Jakobsson E. The cPLA2 C2alpha domain in solution: structure and dynamics of its Ca2+-activated and cation-free states. Biophysical Journal. 92: 966-76. PMID 17085504 DOI: 10.1529/Biophysj.106.091850 |
0.532 |
|
| 2007 |
Saier MH, Hassan KA, Skurray RA, Brown MH, Bapna A, Federici L, Venter H, Luisi B, Fan T, Veen HWv, Lanyi JK, Palma M, Goffeau A, Spencer-Martins I, Baret PV, ... ... Jakobsson E, et al. Contents Vol. 12, 2007 Journal of Molecular Microbiology and Biotechnology. 12: 277-278. DOI: 10.1159/000104694 |
0.533 |
|
| 2007 |
Saier MH, Hassan KA, Skurray RA, Brown MH, Bapna A, Federici L, Venter H, Luisi B, Fan T, Veen HWv, Lanyi JK, Palma M, Goffeau A, Spencer-Martins I, Baret PV, ... ... Jakobsson E, et al. Subject Index Vol. 12, 2007 Journal of Molecular Microbiology and Biotechnology. 12: 276-276. DOI: 10.1159/000104693 |
0.531 |
|
| 2007 |
Tilson JL, Blatecky A, Rendon G, Ger MF, Jakobsson E. MotifNetwork: Genome-wide domain analysis using grid-enabled workflows Proceedings of the 7th Ieee International Conference On Bioinformatics and Bioengineering, Bibe. 872-879. DOI: 10.1109/BIBE.2007.4375662 |
0.471 |
|
| 2007 |
Tilson JL, Rendon G, Ger MF, Jakobsson E. MotifNetwork: A grid-enabled workflow for high-throughput domain analysis of biological sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation Proceedings of the 7th Ieee International Conference On Bioinformatics and Bioengineering, Bibe. 620-627. DOI: 10.1109/BIBE.2007.4375625 |
0.505 |
|
| 2007 |
Marreiro D, Tang Y, Aboud S, Jakobsson E, Saraniti M. Improving the efficiency of BD algorithms for biological systems simulations Journal of Computational Electronics. 6: 377-380. DOI: 10.1007/S10825-006-0129-Z |
0.488 |
|
| 2006 |
Tseng TT, McMahon AM, Zahm RJ, Pacold ME, Jakobsson E. Calcium channel auxiliary subunits. Journal of Molecular Microbiology and Biotechnology. 11: 326-44. PMID 17114897 DOI: 10.1159/000095635 |
0.609 |
|
| 2006 |
Varma S, Chiu SW, Jakobsson E. The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF. Biophysical Journal. 90: 112-23. PMID 16183883 DOI: 10.1529/Biophysj.105.059329 |
0.521 |
|
| 2006 |
Kelley ST, Milton H, Saier i, Ren Q, Nguyen TX, Yen M, Barabote RD, Saier MH, Sigal N, Cohen-Karni D, Siemion S, Bibi E, Tseng T, McMahon AM, Zahm RJ, ... ... Jakobsson E, et al. Contents Vol. 11, 2006 Journal of Molecular Microbiology and Biotechnology. 11: 365-366. DOI: 10.1159/000097268 |
0.533 |
|
| 2006 |
Kelley ST, Milton H, Saier i, Ren Q, Nguyen TX, Yen M, Barabote RD, Saier MH, Sigal N, Cohen-Karni D, Siemion S, Bibi E, Tseng T, McMahon AM, Zahm RJ, ... ... Jakobsson E, et al. Subject Index Vol. 11, 2006 Journal of Molecular Microbiology and Biotechnology. 11: 363-364. DOI: 10.1159/000097267 |
0.531 |
|
| 2005 |
Tasneem A, Iyer LM, Jakobsson E, Aravind L. Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biology. 6: R4. PMID 15642096 DOI: 10.1186/Gb-2004-6-1-R4 |
0.697 |
|
| 2004 |
Malmberg NJ, Varma S, Jakobsson E, Falke JJ. Ca2+ activation of the cPLA2 C2 domain: ordered binding of two Ca2+ ions with positive cooperativity. Biochemistry. 43: 16320-8. PMID 15610026 DOI: 10.1021/Bi0482405 |
0.504 |
|
| 2004 |
Pandit SA, Jakobsson E, Scott HL. Simulation of the early stages of nano-domain formation in mixed bilayers of sphingomyelin, cholesterol, and dioleylphosphatidylcholine. Biophysical Journal. 87: 3312-22. PMID 15339797 DOI: 10.1529/Biophysj.104.046078 |
0.312 |
|
| 2004 |
Pandit SA, Vasudevan S, Chiu SW, Mashl RJ, Jakobsson E, Scott HL. Sphingomyelin-cholesterol domains in phospholipid membranes: atomistic simulation. Biophysical Journal. 87: 1092-100. PMID 15298913 DOI: 10.1529/Biophysj.104.041939 |
0.31 |
|
| 2004 |
Varma S, Jakobsson E. Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues. Biophysical Journal. 86: 690-704. PMID 14747308 DOI: 10.1016/S0006-3495(04)74148-X |
0.558 |
|
| 2004 |
Natarajan S, Varma S, Tang Y, Parker S, Mashl J, Jakobsson E. Toward an integrated computational environment for multiscale computational design of nanoscale Ion Channel semiconductors 2004 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2004. 1: 147-150. |
0.676 |
|
| 2003 |
Mangubat EZ, Tseng TT, Jakobsson E. Phylogenetic analyses of potassium channel auxiliary subunits. Journal of Molecular Microbiology and Biotechnology. 5: 216-24. PMID 12867745 DOI: 10.1159/000071073 |
0.636 |
|
| 2003 |
Shealy RT, Murphy AD, Ramarathnam R, Jakobsson E, Subramaniam S. Sequence-function analysis of the K+-selective family of ion channels using a comprehensive alignment and the KcsA channel structure. Biophysical Journal. 84: 2929-42. PMID 12719225 DOI: 10.1016/S0006-3495(03)70020-4 |
0.367 |
|
| 2003 |
Joseph S, Mashl RJ, Jakobsson E, Aluru NR. Electrolytic Transport in Modified Carbon Nanotubes Nano Letters. 3: 1399-1403. DOI: 10.1021/Nl0346326 |
0.327 |
|
| 2002 |
Jakobsson E, Jay Mashl R, Tseng TT. Investigating ion channels using computational methods Current Topics in Membranes. 52: 255-273. DOI: 10.1016/S1063-5823(02)52011-1 |
0.65 |
|
| 2002 |
Van Der Straaten T, Varma S, Chiu SW, Tang J, Aluru N, Eisenberg R, Ravaioli U, Jakobsson E. Combining computational chemistry and computational electronics to understand protein ion channels 2002 International Conference On Computational Nanoscience and Nanotechnology - Iccn 2002. 60-63. |
0.513 |
|
| 2001 |
Mashl RJ, Scott HL, Subramaniam S, Jakobsson E. Molecular simulation of dioleoylphosphatidylcholine lipid bilayers at differing levels of hydration. Biophysical Journal. 81: 3005-15. PMID 11720971 DOI: 10.1016/S0006-3495(01)75941-3 |
0.31 |
|
| 2001 |
Mashl RJ, Tang Y, Schnitzer J, Jakobsson E. Hierarchical approach to predicting permeation in ion channels. Biophysical Journal. 81: 2473-83. PMID 11606263 DOI: 10.1016/S0006-3495(01)75893-6 |
0.568 |
|
| 1999 |
Chiu SW, Jakobsson E, Subramaniam S, Scott HL. Combined Monte Carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers. Biophysical Journal. 77: 2462-9. PMID 10545348 DOI: 10.1016/S0006-3495(99)77082-7 |
0.307 |
|
| 1999 |
Chiu SW, Subramaniam S, Jakobsson E. Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. I. Structure of the molecular complex. Biophysical Journal. 76: 1929-38. PMID 10096891 DOI: 10.1016/S0006-3495(99)77352-2 |
0.348 |
|
| 1998 |
Jakobsson E. Using theory and simulation to understand permeation and selectivity in ion channels. Methods (San Diego, Calif.). 14: 342-51. PMID 9571089 DOI: 10.1006/Meth.1998.0589 |
0.425 |
|
| 1996 |
Singh C, Sankararamakrishnan R, Subramaniam S, Jakobsson E. Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel. Biophysical Journal. 71: 2276-88. PMID 8913570 DOI: 10.1016/S0006-3495(96)79438-9 |
0.37 |
|
| 1996 |
Novotny JA, Jakobsson E. Computational studies of ion-water flux coupling in the airway epithelium. I. Construction of model. The American Journal of Physiology. 270: C1751-63. PMID 8764159 DOI: 10.1152/Ajpcell.1996.270.6.C1751 |
0.322 |
|
| 1991 |
Chiu SW, Nicholson LK, Brenneman MT, Subramaniam S, Teng Q, McCammon JA, Cross TA, Jakobsson E. Molecular dynamics computations and solid state nuclear magnetic resonance of the gramicidin cation channel. Biophysical Journal. 60: 974-8. PMID 1720680 DOI: 10.1016/S0006-3495(91)82131-2 |
0.342 |
|
| 1991 |
Chiu SW, Jakobsson E, Subramaniam S, McCammon JA. Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophysical Journal. 60: 273-85. PMID 1715766 DOI: 10.1016/S0006-3495(91)82049-5 |
0.355 |
|
| 1991 |
Davenport R, Jakobsson E, Gerber B. Possible dual effect of synapses that are putatively purely excitatory or purely inhibitory: bases in stability theory and implications for neural network behavior. Biological Cybernetics. 65: 47-53. PMID 1715190 DOI: 10.1007/Bf00197289 |
0.317 |
|
| 1990 |
Helfrich P, Jakobsson E. Calculation of deformation energies and conformations in lipid membranes containing gramicidin channels. Biophysical Journal. 57: 1075-84. PMID 1692748 DOI: 10.1016/S0006-3495(90)82625-4 |
0.312 |
|
| 1989 |
Chiu SW, Subramaniam S, Jakobsson E, McCammon JA. Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study. Biophysical Journal. 56: 253-61. PMID 2476188 DOI: 10.1016/S0006-3495(89)82671-2 |
0.379 |
|
| 1989 |
Chiu SW, Jakobsson E. Stochastic theory of singly occupied ion channels. II. Effects of access resistance and potential gradients extending into the bath. Biophysical Journal. 55: 147-57. PMID 2467695 DOI: 10.1016/S0006-3495(89)82786-9 |
0.36 |
|
| 1985 |
Cooper K, Jakobsson E, Wolynes P. The theory of ion transport through membrane channels. Progress in Biophysics and Molecular Biology. 46: 51-96. PMID 2410952 DOI: 10.1016/0079-6107(85)90012-4 |
0.343 |
|
| 1979 |
Jakobsson E. A fully coupled transient excited state model for the sodium channel. II. Implications for action potential generation, threshold, repetitive firing, and accommodation. Journal of Mathematical Biology. 6: 235-48. PMID 750631 DOI: 10.1007/Bf02547799 |
0.344 |
|
| 1979 |
Jakobsson E. A fully coupled transient excited state model for the sodium channel. I. Conductance in the voltage clamped case. Journal of Mathematical Biology. 5: 121-42. PMID 731134 DOI: 10.1007/Bf00275895 |
0.304 |
|
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